Compositions and methods for treating cardiovascular disease and myocardial infarction with dipeptidyl peptidase inhibitors or b type natriuretic peptide analogues resistant to prolyl-specific dipeptidyl degradation

ABSTRACT

The present invention describes compositions and methods for treating cardiovascular disease and myocardial infarction using dipeptidyl peptidase inhibitors. Also provided are methods for increasing natriuretic peptide function by administering one or more analogues of B type natriuretic peptide that provide increased stability in the presence of prolyl-specific dipeptidyl peptidases.

CROSS-REFERENCE

This application is a continuation of U.S. patent application Ser. No.12/391,157, filed on Feb. 23, 2009, which is a continuation of U.S.patent application Ser. No. 11/560,425, filed Nov. 16, 2006, which is acontinuation of U.S. patent application Ser. No. 10/938,760, filed Sep.9, 2004, now U.S. Pat. No. 7,524,635; which claims the benefit of U.S.Provisional Application No. 60/542,086, filed Feb. 4, 2004, and which isa continuation-in-part of U.S. patent application Ser. No. 10/645,874,filed Aug. 20, 2003, and Ser. No. 10/419,059, filed Apr. 17, 2003, whichis a continuation-in-part of U.S. patent application Ser. No.09/835,298, filed Apr. 13, 2001, now U.S. Pat. No. 7,632,647, and Ser.No. 10/139,086, filed May 4, 2002, now U.S. Pat. No. 7,361,473, whichclaims the benefit of U.S. Provisional Application Nos. 60/315,642,filed Aug. 28, 2001, and 60/288,871, filed May 4, 2001; and U.S. patentapplication Ser. No. 10/419,059, filed Apr. 17, 2003, is acontinuation-in-part of International Application No. PCT/US02/26604,filed Aug. 20, 2002, which claims the benefit of U.S. ProvisionalApplication Nos. 60/346,485, filed Jan. 2, 2002, 60/334,964, filed Nov.30, 2001, and 60/313,775, filed Aug. 20, 2001, each to which thisapplication claims priority, and each of which is hereby incorporated byreference in its entirety, including all tables, figures, and claims.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted in ASCII format via EFS-Web and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Nov. 19, 2014 isnamed 36671-744-303-Seqlist.txt and is 7 Kilobytes in size.

FIELD OF THE INVENTION

The present invention relates to medical diagnostics and therapeutics.

BACKGROUND OF THE INVENTION

The following discussion of the background of the invention is merelyprovided to aid the reader in understanding the invention and is notadmitted to describe or constitute prior art to the present invention.

Natriuretic peptides are a group of naturally occurring substances thatact in the body to oppose the activity of the renin-angiotensin system.There are three major natriuretic peptides: atrial natriuretic peptide(ANP), which is synthesized in the atria; brain-type natriuretic peptide(BNP), which is synthesized in the ventricles; and C-type natriureticpeptide (CNP), which is synthesized in the brain.

Mature human A-type natriuretic peptide (ANP) (also referred to asatrial natriuretic peptide) is a biologically active 28 amino acidpeptide that is synthesized, stored, and released by atrial myocytes inresponse to atrial distension, angiotensin II stimulation, endothelin,and sympathetic stimulation (beta-adrenoceptor mediated). Mature ANP isgenerated by proteolytic cleavage of a 128 amino acid precursor molecule(pro-ANP), yielding the biologically active 28 amino acid peptiderepresenting amino acids 99-126 of the pro-ANP molecule (ANP₉₉₋₁₂₆).Linear peptide fragments from the N-terminal prohormone segment havealso been reported to have biological activity.

Mature human B-type natriuretic peptide (BNP) (also called brain-typenatriuretic peptide) is a 32 amino acid, 4 kDa biologically activepeptide that is involved in the natriuresis system to regulate bloodpressure and fluid balance (Bonow, R. O., Circulation 93:1946-1950,1996). The mature BNP hormone is generated by proteolytic cleavage of a108-amino acid precursor molecule, referred to herein as “pro-BNP.”Cleavage generates t a 76-amino acid N-terminal peptide (amino acids1-76), referred to as “NT pro BNP,” and the 32-amino acid maturehormone, referred to as BNP or BNP 32 (amino acids 77-108). It has beensuggested that each of these species—NT pro-BNP, BNP-32, and thepre-pro-BNP—can circulate in human plasma (Tateyama et al., Biochem.Biophys. Res. Commun. 185:760-7, 1992; Hunt et al., Biochem. Biophys.Res. Commun. 214:1175-83, 1995).

Mature human C-type natriuretic peptide (CNP) a 22-amino acid peptidethat is the primary active natriuretic peptide in the human brain; CNPis also considered to be an endothelium-derived relaxant factor, whichacts in the same way as nitric oxide (NO) (Davidson et al., Circulation93:1155-9, 1996). CNP is structurally related to A-type natriureticpeptide (ANP) and B-type natriuretic peptide (BNP); however, while ANPand BNP are synthesized predominantly in the myocardium, CNP issynthesized in the vascular endothelium as a precursor (pro-CNP)(Prickett et al., Biochem. Biophys. Res. Commun. 286:513-7, 2001). CNPis thought to possess vasodilator effects on both arteries and veins andhas been reported to act mainly on the vein by increasing theintracellular cGMP concentration in vascular smooth muscle cells.

ANP and BNP are released in response to atrial and ventricular stretch,respectively, and will cause vasorelaxation, inhibition of aldosteronesecretion in the adrenal cortex, and inhibition of renin secretion inthe kidney. Both ANP and BNP will cause natriuresis and a reduction inintravascular volume, effects amplified by the antagonism ofantidiuretic hormone (ADH). The physiologic effects of CNP differ fromthose of ANP and BNP; CNP has a hypotensive effect, but no significantdiuretic or natriuretic actions. Increased blood levels of natriureticpeptides have been found in certain disease states, suggesting a role inthe pathophysiology of those diseases, including stroke, congestiveheart failure (CHF), cardiac ischemia, systemic hypertension, and acutemyocardial infarction. See, e.g., WO 02/089657; WO 02/083913; and WO03/016910, each of which is hereby incorporated in its entirety,including all tables, figures, and claims. Numerous non-human homologsof the natriuretic peptides are known to those of skill in the art.

The natriuretic peptides, alone, collectively, and/or together withadditional proteins, can serve as disease markers and indicators ofprognosis in various cardiovascular conditions. For example, BNP, whichis synthesized in the cardiac ventricles and correlates with leftventricular pressure, amount of dyspnea, and the state of neurohormonalmodulation, makes this peptide the first potential marker for heartfailure. Measurement of plasma BNP concentration is evolving as a veryefficient and cost effective mass screening technique for identifyingpatients with various cardiac abnormalities regardless of etiology anddegree of LV systolic dysfunction that can potentially develop intoobvious heart failure and carry a high risk of a cardiovascular event.Finding a simple blood test that would aid in the diagnosis andmanagement of patients with CHF clearly would have a favorable impact onthe staggering costs associated with the disease.

Removal of the natriuretic peptides from the circulation is affectedmainly by binding to clearance receptors and enzymatic degradation inthe circulation. See, e.g., Cho et al., Heart Dis. 1: 305-28, 1999;Smith et al., J. Endocrinol. 167: 239-46, 2000. Additionally, humanpro-BNP is reported to be processed in serum such that circulatingpre-pro-BNP is unlikely to be the intact 108 amino acid form. Hunt etal., Peptides 18: 1475-81, 1997. Degradation of the natriuretic peptidesis believed mediated by neutral endopeptidase. For example, Norman etal. (Biochem. Biophys. Res. Commun. 28: 175: 22-30, 1991) report thatneutral endopeptidase can cleave human BNP between residues 2 and 3,between residues 4 and 5, and between residues 17 and 18. Similarly,Lindberg and Andersson (Regul. Pept. 47: 53-63, 1993) report that humanANP is cleaved between residues 3 and 4 and residues 14 and 15. Thebiological activity of this hydrolyzed product was about 500-fold lessthan intact ANP. Additionally, Knecht et al. (Life Sci. 71: 2701-12,2002) report that renal neutral endopeptidase is upregulated in heartfailure, a condition where natriuretic peptide levels are increased. Forthis reason, neutral endopeptidase has been targeted for inhibition intreatment of cardiovascular disease. See, e.g., Corti et al.,Circulation 104: 1856-62, 2001.

Confusion over the stability of the natriuretic peptides, particularlyin blood-derived samples (e.g., serum, plasma, whole blood) has beenreported. ANP is reported to be a better substrate for neutralendopeptidase than is BNP. Similarly, Shimizu et al. (Clin. Chem. Acta305: 181-6, 2001), Gobinet-Georges et al. (Clin. Chem. Lab. Med. 38:519-23, 2000) and Murdoch et al. (Heart 78: 594-7, 1997) report that BNPis stable in certain blood-derived samples or when blood is collectedunder certain conditions. A more recent report by Shimizu et al. (Clin.Chem. Acta 316: 129-35, 2002) indicates that 94% of BNP in whole bloodwas a digested form in which 2 amino terminal residues had been removed;and that BNP in plasma was degraded to a number of unidentified forms.

SUMMARY OF THE INVENTION

The present invention relates in part to compositions and methodsdesigned to determine the presence or amount of biologically activenatriuretic peptides, or their fragments, in a sample. The degradationof natriuretic peptides is an ongoing process that may be a function of,inter alia, the elapsed time between onset of an event triggeringnatriuretic peptide release into the tissues and the time the sample isobtained or analyzed; the quantity of proteolytic enzymes present; etc.This degradation can produce circulating amounts of natriuretic peptideshaving reduced or lost biological function (referred to herein forconvenience as “inactive fragments” of a natriuretic peptide).

Failure to consider this degradation when designing an assay for one ormore natriuretic peptides may result in an assay that detects bothbiologically active forms of a natriuretic peptide(s) of interest, aswell as inactive fragments of the natriuretic peptide(s). This may leadto the conclusion that an assay shows particularly good stability (i.e.,the analyte of interest is not lost to the assay during sample storage),when in fact the natriuretic peptide of interest is actually beingdegraded to an inactive fragment and the assay result is confounded bythe inability to distinguish the intended analyte from the pool ofinactive fragments originally present in the sample. Because thebiologically active forms may be more relevant to the physiologic stateof the subject, and because upregulated proteolytic enzymes in diseasedsubjects may lead to particularly large pools of inactive fragments inthe subjects of potentially the greatest interest, the compositions andmethods described herein may provide improved diagnostic and prognosticinformation to the artisan in comparison to assays that are not specificfor the biologically active forms.

The methods and compositions described herein can meet the need in theart for rapid, sensitive and specific diagnostic assay to be used in thediagnosis and differentiation of various cardiovascular diseases,including stroke, congestive heart failure (CHF), cardiac ischemia,systemic hypertension, and/or acute myocardial infarction. Moreover, themethods and compositions of the present invention can also be used tofacilitate the treatment of patients and the development of additionaldiagnostic and/or prognostic indicators and indicator panels.

In a first aspect then, the present invention relates to methods fordetecting the presence or amount of a natriuretic peptide in a sample,comprising performing an assay that detects a biologically activenatriuretic peptide, but that exhibits at least a 5-fold reduction insignal from, and preferably does not appreciably detect, one or morebiologically inactive fragments of the natriuretic peptide. Biologicallyinactive fragments may include those in which residues from either orboth of the N-terminus or C-terminus of the biologically activenatriuretic peptide have been removed, and/or in which the loop formedby intramolecular disulfide bonding of the natriuretic peptide has beencleaved. Such biologically inactive fragments may be formed, forexample, by cleaving one or more peptide bonds in the biologicallyactive natriuretic peptide.

In related aspects, the present invention relates to methods fordetecting the presence or amount of a natriuretic peptide in a sample,comprising performing an assay that detects an intact natriureticpeptide, but that exhibits at least a 5-fold reduction in signal from,and preferably does not appreciably detect, an equimolar amount of apeptide that is generated when a portion, and preferably at least anN-terminal portion, of the intact natriuretic peptide is removed.

In various embodiments, the present invention relates to methods fordetecting the presence or amount of BNP in a sample, comprisingperforming an assay that detects BNP₇₇₋₁₀₈, but that exhibits at least a5-fold reduction in signal from, and preferably does not appreciablydetect, an equimolar amount of BNP₉₄₋₁₀₈; the assay detects BNP₇₇₋₁₀₈,but exhibits at least a 5-fold reduction in signal from, and preferablydoes not appreciably detect, BNP₉₀₋₁₀₈; the assay detects BNP₇₇₋₁₀₈, butexhibits at least a 5-fold reduction in signal from, and preferably doesnot appreciably detect, BNP₈₁₋₁₀₈; the assay detects BNP₇₇₋₁₀₈, butexhibits at least a 5-fold reduction in signal from, and preferably doesnot appreciably detect, BNP₇₉₋₁₀₈; the assay detects BNP₇₇₋₁₀₈, butexhibits at least a 5-fold reduction in signal from, and preferably doesnot appreciably detect, BNP₇₇₋₁₀₆; and/or the assay detects BNP₇₇₋₁₀₈,but exhibits at least a 5-fold reduction in signal from, and preferablydoes not appreciably detect, BNP₇₉₋₁₀₆.

In various additional embodiments, the present invention relates tomethods for detecting the presence or amount of BNP in a sample,comprising performing an assay that detects BNP₁₋₇₆, but that exhibitsat least a 5-fold reduction in signal from, and preferably does notappreciably detect, an equimolar amount of BNP₃₈₋₇₆; the assay detectsBNP₁₋₇₆, but exhibits at least a 5-fold reduction in signal from, andpreferably does not appreciably detect, BNP₂₄₋₇₆; the assay detectsBNP₁₋₇₆, but exhibits at least a 5-fold reduction in signal from, andpreferably does not appreciably detect, BNP₁₂₋₇₆; the assay detectsBNP₁₋₇₆, but exhibits at least a 5-fold reduction in signal from, andpreferably does not appreciably detect, BNP₃₋₇₆; the assay detectsBNP₁₋₇₆, but exhibits at least a 5-fold reduction in signal from, andpreferably does not appreciably detect, BNP₁₋₇₃; and/or the assaydetects BNP₁₋₇₆, but exhibits at least a 5-fold reduction in signalfrom, and preferably does not appreciably detect, BNP₃₋₇₃.

In still other additional embodiments, the present invention relates tomethods for detecting the presence or amount of ANP in a sample,comprising performing an assay that detects ANP₉₉₋₁₂₆, but that exhibitsat least a 5-fold reduction in signal from, and preferably does notappreciably detect, an equimolar amount of ANP₁₁₃₋₁₂₆; the assay detectsANP₉₉₋₁₂₆, but exhibits at least a 5-fold reduction in signal from, andpreferably does not appreciably detect, ANP₁₀₅₋₁₂₆; the assay detectsANP₉₉₋₁₂₆, but exhibits at least a 5-fold reduction in signal from, andpreferably does not appreciably detect, ANP₁₀₂₋₁₂₆, the assay detectsANP₉₉₋₁₂₆, but exhibits at least a 5-fold reduction in signal from, andpreferably does not appreciably detect, ANP₉₉₋₁₂₄; and/or the assaydetects ANP₉₉₋₁₂₆, but exhibits at least a 5-fold reduction in signalfrom, and preferably does not appreciably detect, ANP₁₀₂₋₁₂₄.

As described hereinafter, such assays may be designed in a variety ofways known to those of skill in the art. Preferred assays areimmunoassays, although other methods are well known to those skilled inthe art (for example, the use of biosensors, or the use of naturalreceptors for natriuretic peptides that are known in the art). Anysuitable immunoassay may be utilized, for example, assays which directlydetect analyte binding (e.g., by ellipsometric detection), enzyme-linkedimmunoassays (ELISA), radioimmunoassays (RIAs), competitive bindingassays, sandwich immunoassays, and the like. Specific immunologicalbinding of the antibody to the one or more natriuretic peptide fragmentscan be detected directly or indirectly. Direct labels includefluorescent or luminescent tags, metals, dyes, radionuclides, and thelike, attached to the antibody. Indirect labels include various enzymeswell known in the art, such as alkaline phosphatase, horseradishperoxidase and the like. Antibodies attached to a second molecule, suchas a detectable label, are referred to herein as “antibody conjugates.”The skilled artisan will also understand that natural receptors for thenatriuretic peptides exist, and that these receptors may also be used ina manner akin to antibodies in providing binding assays.

Immunoassays may be formulated using one or more antibodies selected tobind to an epitope that is partially or completely lost frombiologically inactive fragments of the natriuretic peptide as comparedto the intact natriuretic peptide. For example, in a sandwich assay, ifan antibody bound to a solid phase is selected to bind preferentially tothe N-terminal portion of the molecule, and a labeled antibody isselected to bind to the C-terminal portion of the molecule, only thosemolecules that contain both the N- and C-terminal portions of themolecule will be detected in the assay. Alternatively, both the solidphase and labeled antibodies may be selected to bind to the N-terminalportion of the molecule.

The skilled artisan will understand that cleavage of the natriureticpeptide may remove all of the epitope to which an antibody binds (e.g.,the antibody binds to the N-terminal region alone). Alternatively, anepitope may be formed from portions of the natriuretic peptide that arenot contiguous in the linear sequence of the molecule, but that areassociated in 3-dimensional space in solution, so that epitope comprisesmore than the described amino acid residues, but removal of the regiondescribed amino acid residues results in reduced binding of theantibody, and hence a loss of signal in the assay.

In certain embodiments, antibodies are selected, based not upon aparticular affinity for one or more natriuretic peptide(s), but insteadbased upon a signal that is obtainable in a binding assay such as animmunoassay. The skilled artisan will recognize that various bindingassay formats are known in the art, and that it is often the use ofantibodies to formulate an appropriate assay that is more important thana particular affinity of an antibody for one or more target molecules.For example, competitive binding assays may comprise a receptor (e.g.,an antibody) bound to a solid surface. An analyte of interest in a testsample competes for binding with a labeled molecule that also binds tothe receptor. The amount of labeled molecule bound to the receptor (andhence assay signal) is inversely proportional to the amount of analyteof interest in the test sample. In this case, a single antibody attachedto the solid phase is used. Alternatively, in a sandwich immunoassay, afirst antibody, typically bound to a solid surface, and a secondantibody, typically conjugated to a detectable label, each bind to ananalyte of interest in a test sample. The amount of labeled moleculebound to the receptor (and hence assay signal) is directly proportionalto the amount of analyte of interest in the test sample.

The immunoassays of the present invention are preferably designed todistinguish a biologically active natriuretic peptide from abiologically inactive natriuretic peptide and/or an intact natriureticpeptide from a natriuretic peptide fragment. For example, a preferredimmunoassay would distinguish a natriuretic peptide comprising an intactN-terminal region from a fragment of the natriuretic peptide from whichthe N-terminal region has been lost. An immunoassay is said to“distinguish” between a first group of polypeptides and a second groupof polypeptides if the immunoassay provides a signal related to bindingof the first group of polypeptides that is at least a factor of 5greater than a signal obtained from an equal number of molecules of thesecond group of polypeptides under the same assay conditions, when theassay is performed at no more than twice the amount of the first groupof polypeptides necessary to obtain a maximum signal. More preferably,the signal is at least a factor of 10 greater, even more preferably atleast a factor of 20 greater, and most preferably at least a factor of50 greater, at least a factor of 100 greater, or more under such assayconditions. An assay does not “appreciably detect” the second group ofpolypeptides if a signal related to binding of the first group ofpolypeptides may be obtained, but no signal above background is obtainedfrom an equal number of molecules of the second group of polypeptidesunder such assay conditions.

In another aspect, the present invention relates to methods fordetecting the presence or amount of a natriuretic peptide in a sample,comprising performing an assay in which the signal depends upon anantibody that specifically binds to a biologically active natriureticpeptide, but that does not specifically bind to biologically inactivefragments of the natriuretic peptide. As discussed above, biologicallyinactive fragments may include those in which residues from either orboth of the N-terminus or C-terminus of the intact natriuretic peptidehave been removed, and/or in which the loop formed by intramoleculardisulfide bonding of the natriuretic peptide has been cleaved. Inpreferred embodiments, the assay is performed under conditions in whichthe signal depends upon an antibody that specifically binds to theintact natriuretic peptide, but that does not specifically bind to apeptide that is generated from the natriuretic peptide when anN-terminal portion of the natriuretic peptide is removed.

In related aspects, the present invention relates to methods fordetecting the presence or amount of a natriuretic peptide in a sample,comprising performing an assay in which the signal depends upon anantibody that specifically binds to the intact natriuretic peptide, butthat does not specifically bind to fragments of the natriuretic peptidegenerated when a portion, and preferably at least an N-terminal portion,of the natriuretic peptide is removed.

In various embodiments, the present invention relates to methods fordetecting the presence or amount of BNP in a sample, comprisingperforming an assay in which the signal depends upon an antibody thatspecifically binds to BNP₇₇₋₁₀₈, but that does not specifically bind toBNP₉₄₋₁₀₈; the assay depends upon an antibody that specifically binds toBNP₇₇₋₁₀₈, but does not specifically bind to BNP₉₀₋₁₀₈; the assaydepends upon an antibody that specifically binds to BNP₇₇₋₁₀₈, but doesnot specifically bind to BNP₈₁₋₁₀₈; the assay depends upon an antibodythat specifically binds to BNP₇₇₋₁₀₈, but does not specifically bind toBNP₇₉₋₁₀₈; the assay depends upon an antibody that specifically binds toBNP₇₇₋₁₀₈, but does not specifically bind to BNP₇₇₋₁₀₆; and/or the assaydepends upon an antibody that specifically binds to BNP₇₇₋₁₀₈, but doesnot specifically bind to BNP₇₉₋₁₀₆.

In various additional embodiments, the present invention relates tomethods for detecting the presence or amount of BNP in a sample,comprising performing an assay in which the signal depends upon anantibody that specifically binds to BNP₁₋₇₆, but that does notspecifically bind to BNP₃₈₋₇₆; the assay depends upon an antibody thatspecifically binds to BNP₁₋₇₆, but does not specifically bind toBNP₂₄₋₇₆; the assay depends upon an antibody that specifically binds toBNP₁₋₇₆, but does not specifically bind to BNP₁₂₋₇₆; the assay dependsupon an antibody that specifically binds to BNP₁₋₇₆, but does notspecifically bind to BNP₃₋₇₆; the assay depends upon an antibody thatspecifically binds to BNP₁₋₇₆, but does not specifically bind toBNP₁₋₇₃; and/or the assay depends upon an antibody that specificallybinds to BNP₁₋₇₆, but does not specifically bind to BNP₃₋₇₃.

In other additional embodiments, the present invention relates tomethods for detecting the presence or amount of ANP in a sample,comprising performing an assay in which the signal depends upon anantibody that specifically binds to ANP₉₉₋₁₂₆, but that does notspecifically bind to ANP₁₁₃₋₁₂₆; the assay depends upon an antibody thatspecifically binds to ANP₉₉₋₁₂₆, but that does not specifically bind toANP₁₀₅₋₁₂₆; the assay depends upon an antibody that specifically bindsto ANP₉₉₋₁₂₆, but that does not specifically bind to ANP₁₀₂₋₁₂₆; theassay depends upon an antibody that specifically binds to ANP₉₉₋₁₂₆, butthat does not specifically bind to ANP₉₉₋₁₂₄; and/or the assay dependsupon an antibody that specifically binds to ANP₉₉₋₁₂₆, but that does notspecifically bind to ANP₁₀₂₋₁₂₄.

A signal from an immunoassay is said to “depend upon binding to anantibody” if the antibody participates in formation of a complexnecessary to generate the signal. For example, in a sandwich immunoassayformulated using a solid phase antibody and a second antibody conjugate,each of which must bind to an analyte to form the sandwich, each of thesolid phase antibody and second antibody participate in formation of thecomplex necessary to generate the signal. In a competitive immunoassaywhere a single antibody is used, and an analyte competes with an analyteconjugate for binding, the single antibody participates in formation ofthe complex necessary to generate the signal. The skilled artisan willunderstand that numerous additional immunoassay formulations may beprovided.

The assay methods described herein may also comprise a step of storing asample for a period of time prior to assay for one or more natriureticpeptides. Because degradation of natriuretic peptides may be an ongoingprocess during storage, the storage considerations should be selected toreduce loss of the N-terminal portion of the molecule. Thus, the storageconditions may comprise addition of one or more inhibitors ofnatriuretic peptide degradation. As discussed hereinafter, the storageconditions may comprise one or more inhibitors of neutral endopeptidaseand/or one or more inhibitors of prolyl-specific dipeptidyl peptidase.Such inhibitors are well known in the art. See, e.g., Corti et al.,Circulation 104: 1856-62, 2001; Senten et al., J. Comb. Chem. 5: 336-44,2003; Senten et al., Bioorg. Med. Chem. Lett. 12: 2825-8, 2002. In analternative or in conjunction with such inhibitors, storage conditionsmay comprise storage at a reduced temperature, preferably below thefreezing point of the sample.

In another aspect, the present invention relates to an assay deviceconfigured and arranged to perform the described assays. Devices forperforming the assays described herein preferably contain a plurality ofdiscrete, independently addressable locations, or “diagnostic zones,”each of which is related to a particular analyte or set of analytes ofinterest, one or more of which is a natriuretic peptide. For example,each of a plurality of discrete zones may comprise a receptor (e.g., anantibody) for binding a different analyte. Following reaction of asample with the devices, a signal is generated from the diagnosticzone(s), which may then be correlated to the presence or amount of thepeptide of interest.

In yet another aspect, the presence or amount of one or more natriureticpeptide(s) of interest measured by the methods described herein may berelated to the presence or absence of a disease, or a disease prognosis(e.g., the likelihood of a future adverse outcome related to a disease).Preferred diseases include various cardiovascular and cerebrovasculardiseases, including stroke, congestive heart failure (CHF), cardiacischemia, systemic hypertension, and/or acute myocardial infarction.These methods preferably comprise determining the presence or amount ofone or more natriuretic peptide(s) by the methods described herein, andrelating that presence or amount to the disease or prognosis ofinterest.

In certain embodiments, the signal obtained from an assay need not berelated to the presence or amount of one or more natriuretic peptide(s);rather, the signal may be directly related to the presence or absence ofa disease, or the likelihood of a future adverse outcome related to adisease. For example, a level of signal x may indicate that y pg/mL of anatriuretic peptide is present in the sample. A table may then indicatethat y pg/mL of that natriuretic peptide indicates congestive heartfailure. It may be equally valid to simply relate a level of signal xdirectly to congestive heart failure, without determining how much ofthe natriuretic peptide is present. Such a signal is preferably obtainedfrom an immunoassay using the antibodies of the present invention,although other methods are well known to those skilled in the art.

In still another aspect, the present invention relates to methods forselecting one or more antibodies for use in an assay for natriureticpeptide(s). These methods comprise selecting antibodies that, when usedin an assay, detect a biologically active natriuretic peptide ofinterest, but that exhibit at least a 5-fold reduction in signal from,and preferably do not appreciably detect, biologically inactivefragments of the natriuretic peptide. As above, biologically inactivefragments may include those in which residues from either or both of theN-terminus or C-terminus of the intact natriuretic peptide have beenremoved, and/or in which the loop formed by intramolecular disulfidebonding of the natriuretic peptide has been cleaved.

In related aspects, the present invention relates to methods for forselecting one or more antibodies for use in an assay, comprisingselecting antibodies that, when used in an assay, detect an intactnatriuretic peptide of interest, but that exhibit at least a 5-foldreduction in signal from, and preferably do not appreciably detect, anequimolar amount of a peptide that is generated from the natriureticpeptide when a portion, and preferably an N-terminal portion, of thenatriuretic peptide is removed.

In various embodiments, the methods comprise selecting one or moreantibodies that detect BNP₇₇₋₁₀₈ when used in an assay, but that exhibitat least a 5-fold reduction in signal from, and preferably do notappreciably detect, an equimolar amount of BNP₉₄₋₁₀₈; selecting one ormore antibodies that detect BNP₇₇₋₁₀₈, but that exhibit at least a5-fold reduction in signal from, and preferably do not appreciablydetect, BNP₉₀₋₁₀₈, selecting one or more antibodies that detectBNP₇₇₋₁₀₈, but that exhibit at least a 5-fold reduction in signal from,and preferably do not appreciably detect, BNP₈₁₋₁₀₈; selecting one ormore antibodies that detect BNP₇₇₋₁₀₈, but that exhibit at least a5-fold reduction in signal from, and preferably do not appreciablydetect, BNP₇₉₋₁₀₈; selecting one or more antibodies that detectBNP₇₇₋₁₀₈, but that exhibit at least a 5-fold reduction in signal from,and preferably do not appreciably detect, BNP₇₇₋₁₀₆; and/or selectingone or more antibodies that detect BNP₇₇₋₁₀₈, but that exhibit at leasta 5-fold reduction in signal from, and preferably do not appreciablydetect, BNP₇₉₋₁₀₆.

In various additional embodiments, the methods comprise selecting one ormore antibodies that detect BNP₁₋₇₆, when used in an assay, but thatexhibit at least a 5-fold reduction in signal from, and preferably donot appreciably detect, an equimolar amount of BNP₃₈₋₇₆; selecting oneor more antibodies that detect BNP₁₋₇₆, but that exhibit at least a5-fold reduction in signal from, and preferably do not appreciablydetect, BNP₂₄₋₇₆; selecting one or more antibodies that detect BNP₃₁₋₇₆,but that exhibit at least a 5-fold reduction in signal from, andpreferably do not appreciably detect, BNP₁₂₋₇₆; selecting one or moreantibodies that detect BNP₁₋₇₆, but that exhibit at least a 5-foldreduction in signal from, and preferably do not appreciably detect,BNP₃₋₇₆; selecting one or more antibodies that detect BNP₁₋₇₆, but thatexhibit at least a 5-fold reduction in signal from, and preferably donot appreciably detect, BNP₁₋₇₃; and/or selecting one or more antibodiesthat detect BNP₁₋₇₆, but that exhibit at least a 5-fold reduction insignal from, and preferably do not appreciably detect, BNP₃₋₇₃.

In other additional embodiments, the methods comprise selecting one ormore antibodies that detect ANP₉₉₋₁₂₆ when used in an assay, but thatexhibit at least a 5-fold reduction in signal from, and preferably donot appreciably detect, an equimolar amount of ANP₁₁₃₋₁₂₆; selecting oneor more antibodies that detect ANP₉₉₋₁₂₆ when used in an assay, but thatexhibit at least a 5-fold reduction in signal from, and preferably donot appreciably detect, an equimolar amount of ANP₁₀₅₋₁₂₆; selecting oneor more antibodies that detect ANP₉₉₋₁₂₆ when used in an assay, but thatexhibit at least a 5-fold reduction in signal from, and preferably donot appreciably detect, an equimolar amount of ANP₁₀₁₋₁₂₆; selecting oneor more antibodies that detect ANP₉₉₋₁₂₆ when used in an assay, but thatexhibit at least a 5-fold reduction in signal from, and preferably donot appreciably detect, an equimolar amount of ANP₉₉₋₁₂₄; and/orselecting one or more antibodies that detect ANP₉₉₋₁₂₆ when used in anassay, but that exhibit at least a 5-fold reduction in signal from, andpreferably do not appreciably detect, an equimolar amount of ANP₁₀₁₋₁₂₄.

In other related aspects, the present invention relates to a method ofselecting one or more antibodies for use in an assay for natriureticpeptide(s). The methods comprise selecting one or more antibodies thatspecifically bind to a biologically active natriuretic peptide, but thatdo not specifically bind to biologically inactive fragments of thenatriuretic peptide. As discussed above, biologically inactive fragmentsmay include those in which residues from either or both of theN-terminus or C-terminus of the intact natriuretic peptide have beenremoved, and/or in which the loop formed by intramolecular disulfidebonding of the natriuretic peptide has been cleaved. In preferredembodiments, the assay is performed under conditions in which the signaldepends upon an antibody that specifically binds to the intactnatriuretic peptide, but that does not specifically bind to a peptidethat is generated from the natriuretic peptide when an N-terminalportion of the natriuretic peptide is removed

In still other related aspects, the present invention relates to methodsfor for selecting one or more antibodies for use in an assay, comprisingselecting antibodies that specifically bind to the intact natriureticpeptide, but that do not specifically bind to biologically inactivefragments of the natriuretic peptide generated when an N-terminalportion of the natriuretic peptide is removed.

In various embodiments, the methods comprise selecting one or moreantibodies that specifically bind to BNP₇₇₋₁₀₈, but that do notspecifically bind to BNP₉₄₋₁₀₈; selecting one or more antibodies thatspecifically bind to BNP₇₇₋₄₀₈, but that do not specifically bind toBNP₉₀₋₁₀₈; selecting one or more antibodies that specifically bind toBNP₇₇₋₁₀₈, but that do not specifically bind to BNP₈₁₋₁₀₈; selecting oneor more antibodies that specifically bind to BNP₇₇₋₁₀₈, but that do notspecifically bind to BNP₇₉₋₁₀₈; selecting one or more antibodies thatspecifically bind to BNP₇₇₋₁₀₈, but that do not specifically bind toBNP₇₇₋₁₀₆; and/or selecting one or more antibodies that specificallybind to BNP₇₇₋₁₀₈, but that do not specifically bind to BNP₇₉₋₁₀₆.

In various additional embodiments, the methods comprise selecting one ormore antibodies that specifically bind to BNP₁₋₇₆, but that do notspecifically bind to BNP₃₈₋₇₆; selecting one or more antibodies thatspecifically bind to BNP₁₋₇₆, but that do not specifically bind toBNP₂₄₋₇₆; selecting one or more antibodies that specifically bind toBNP₁₋₇₆, but that do not specifically bind to BNP₁₂₋₇₆, selecting one ormore antibodies that specifically bind to BNP₁₋₇₆, but that do notspecifically bind to BNP₃₋₇₆; selecting one or more antibodies thatspecifically bind to BNP₁₋₇₆, but that do not specifically bind toBNP₁₋₇₃; and/or selecting one or more antibodies that specifically bindto BNP₁₋₇₆, but that do not specifically bind to BNP₃₋₇₃.

In other additional embodiments, the methods comprise selecting one ormore antibodies that specifically bind to ANP₉₉₋₁₂₆, but that do notspecifically bind to ANP₁₁₃₋₁₂₆; selecting one or more antibodies thatspecifically bind to ANP₉₉₋₁₂₆, but that do not specifically bind toANP₁₀₅₋₁₂₆; selecting one or more antibodies that specifically bind toANP₉₉₋₁₂₆, but that do not specifically bind to ANP₁₀₁₋₁₂₆; selectingone or more antibodies that specifically bind to ANP₉₉₋₁₂₆, but that donot specifically bind to ANP₉₉₋₁₂₄; and/or selecting one or moreantibodies that specifically bind to ANP₉₉₋₁₂₆, but that do notspecifically bind to ANP₁₀₁₋₁₂₄.

In another aspect, one or more antibodies and/or antibody conjugates ofthe present invention may be provided as kits for determining thepresence or amount of natriuretic peptide(s). These kits preferablycomprise devices and reagents for performing at least one assay asdescribed herein on a test sample. Such kits preferably containsufficient reagents to perform one or more such determinations, and/orFood and Drug Administration (FDA)-approved labeling.

In still another aspect, the invention relates to methods fordetermining a treatment regimen for use in a patient. The methodspreferably comprise determining the presence or amount of one or morenatriuretic peptide(s) by the methods described herein, and relatingthis presence or amount to a disease or prognostic state. As discussedherein, diagnosis and differentiation of various cardiovascular andcerebrovascular diseases, including stroke, congestive heart failure(CHF), cardiac ischemia, systemic hypertension, acute coronary syndrome,and/or acute myocardial infarction may be related to ANP, BNP, and/orCNP levels. Once a diagnosis or prognosis is obtained, a treatmentregimen is selected to be consistent with that diagnosis.

It is another object of the invention to provide compositions andmethods for stabilizing natriuretic peptides. Such methods may improvethe therapeutic potential of natriuretic peptides, particularly for thetreatment of cardiovascular diseases. Several natriuretic peptides,including pro-BNP, mature BNP, and pro-ANP comprise a penultimateproline residue, and are suitable substrates for prolyl-specificdipeptidyl dipeptidases (“DPPs”). Thus, while mature BNP has beenreported to exhibit resistance to degradation by neutral endopeptidaserelative to ANP, DPPs may represent a previously unrecognizeddegradation pathway for the mature BNP molecule as well as for pro-BNPand pro-ANP. Furthermore, the removal of the proline-containingdipeptide may open the various natriuretic peptides to furtherdegradation by other peptidases. Subjects that may benefit fromincreased natriuretic peptide concentrations may be treated withinhibitors of one or more DPPs, either alone or in combination withneutral endopeptidase inhibitors, and/or treated with natriureticpeptides and/or natriuretic peptide analogs exhibiting increased DPPstability. In addition, BNP in samples removed from a subject may bestabilized during storage using these same inhibitors.

Thus, in one aspect, the present invention relates to methods ofinhibiting degradation of one or more natriuretic peptides. The methodcomprises administering one or more inhibitors of prolyl-specific DPP inan amount sufficient to inhibit degradation of the natriuretic peptide.

In another aspect, the present invention relates to methods for treatinga subject in need of increased natriuretic peptide function, preferablysubjects suffering from heart failure. The methods compriseadministering one or more inhibitors of prolyl-specific DPP to thesubject, preferably in an amount sufficient to inhibit degradation ofthe natriuretic peptide.

In certain embodiments, the inhibitor(s) of prolyl-specific DPP areselective for one or more DPP(s) for which pro-BNP, mature BNP, and/orpro-ANP are a substrate. Methods for designing and selecting specificDPP inhibitors are well known in the art. See, e.g., Leiting et al.,Biochem. J. 371: 525-32, 2003; Sedo et al., Physiol. Res. 52: 367-72,2003; Villhauer et al., J. Med. Chem. 46: 2774-89, 2003; Senten et al.,J. Comb. Chem. 5: 336-44, 2003; Senten et al., Bioorg. Med. Chem. Lett.12: 2825-8, 2002; Borloo and Meester, Verh. K. Acad. Geneeskd. Belg. 56:57-88, 1994. In addition, DPP may be inhibited at the level ofexpression by methods known to those of skill in the art, such as byantisense or RNAi constructs. DPPs may also be inhibited through the useof binding proteins, e.g., antibodies or fragments thereof thatspecifically bind to one or more DPPs and prevent their activity on anatriuretic peptide substrate.

The methods described herein may comprise the use of one or moreinhibitors of prolyl-specific DPP alone, or such inhibitors may becombined with one or more inhibitors of neutral endopeptidase and/orother protease inhibitors, and/or with one or more exogenously addednatriuretic peptides to provide a potentiated increase in natriureticpeptide function to the subject in comparison to the use of inhibitorsof neutral endopeptidase and/or exogenously added natriuretic peptidesin the absence of prolyl-specific DPP inhibitor(s). These compounds maybe conveniently provided as part of a pharmaceutical composition.

In preferred embodiments, subjects receiving the treatment methodsdescribed herein suffer from diseases selected from the group consistingof stroke, congestive heart failure (CHF), cardiac ischemia, systemichypertension, and/or acute myocardial infarction. In particularlypreferred embodiments, subjects receiving the treatment methodsdescribed herein are selected on the basis of a BNP level. For example,subjects may be selected on the basis of a plasma BNP level prior toreceiving treatment of at least about 80 pg/mL, preferably at leastabout 100 pg/mL, still more preferably at least about 200 pg/mL, yetmore preferably at least about 500 pg/mL, and most preferably at leastabout 1000 pg/mL.

In yet another aspect, the present invention relates to methods fortreating a subject in need of increased natriuretic peptide functioncomprising administering one or more analogues of a natriuretic peptidethat provide increased stability in the presence of prolyl-specific DPP(e.g. as measured by an increase in the t_(1/2) of the natriureticpeptide of interest in the blood of the subject).

It is yet another object of the invention to provide methods andcompositions for determining the presence or amount of one or morenatriuretic peptides of interest, where one or more of those natriureticpeptides of interest are glycosylated. Covalently bound carbohydrateresidues in glycosylated natriuretic peptides can have substantialeffects on the ability of various assay methods to detect such peptides.By careful selection of assay conditions, such effects can be mitigated,resulting in an assay result that is representative of the presence oramount of the natriuretic peptides of interest in a sample.

Thus, in another aspect, the present invention relates to methods fordetecting the presence or amount of one or more natriuretic peptides ofinterest in a sample, where one or more of those natriuretic peptidescomprise covalently bound carbohydrate residues. These methods compriseremoving one or more covalently bound carbohydrate residues from one ormore of said natriuretic peptides of interest, and assaying the samplefor the natriuretic peptides of interest. The assay result is thusrelated to the presence or amount of said natriuretic peptides ofinterest in said sample. In various embodiments, the covalently boundcarbohydrate residues may be removed from one or more naturieticpeptides by enzymatic treatment of the peptides, by non-enzymaticchemical treatment of the peptides, or by a combination of thesemethods.

Effective enzymatic methods for removing N- and O-linked carbohydrateresidues are well known in the art, using enzymes such as N-glycanase(also known as N-glycosidase), endoglycosidase H, endoglycosidase A,O-glycanase (also known as endo-α-N-acetylgalactosaminidase),α2-(3,6,8,9)-neuriminidase, β(1,4)-galactosidase,N-acetylglucosaminidase, endoglycosidase F₁, endoglycosidase F₂, and/orendoglycosidase F₃. This list is not meant to be limiting.

In the case of non-enzymatic chemical treatments for removal ofcovalently bound carbohydrate residues from peptides, hydrazinehydrolysis has been found to be effective in the release of unreduced O-and N-linked oligosaccharides. Selective and sequential release ofoligosaccharides can be accomplished by initial mild hydrazinolysis ofthe O-linked oligosaccharides at about 60° C. followed by N-linkedoligosaccharides at about 95° C. See, e.g., Patel and Rarekh, Meth.Enzymol. 230, 58-66, 1994. Such treatment may result in destruction ofthe polypeptide however. Alkaline-β-elimination of O-linkedoligosaccharides, which utilizes alkaline sodium borohydride in a mildbase environment, may be preferred. See, e.g., Glycobiology: A PracticalApproach, Fukuda, M. and Kobata, A. (Eds), pp. 291-328, IRL/Oxford Univ.Press, Oxford, 1993. In addition, Trifluoromethanesulfonic acidhydrolysis may be employed. This method typically leaves an intactpolypeptide, but results in destruction of the glycan. See, e.g., Edge,Biochem. 1 376: 339-50, 2003.

The foregoing methods of sugar removal from peptides may be used onnative (non-denatured) polypeptides and/or following denaturation of thepolypeptides. Whether enzymatic, non-enzymatic, or both treatments areemployed to remove covalently bound carbohydrate residues fromnatriuretic peptides, it is preferred that at least about 50%, morepreferably, at least about 60%, still more preferably at least about70%, yet more preferably at least about 80%, and most preferably atleast about 90% to about 100% of the carbohydrate residues are removedfrom one or more, and preferably all, of the glycosylated natriureticpeptides of interest by this treatment. The extent of glycosylation of apolypeptide can be determined by comparing the apparent mass of thepolypeptide to the mass of the amino acid constituents of thepolypeptide, and assuming that the balance of the apparent mass iscontributed by glycosylation. In the event that other modifications(e.g., oxidation, nitration, phosphorylation) are known to haveoccurred, the mass contributed by these other modifications may also besubtracted from the apparent mass. The extent of carbohydrate residueremoval can then be monitored by determining the apparent mass of thepolypeptide following deglycosylation treatment. Methods for determiningthe apparent mass of a polypeptide (e.g., SDS gel electrophoresis,analytical centrifugation, gel permeation chromatography, massspectrometry, etc.) are well known to those of skill in the art.

The sample containing such glycosylated natriuretic peptides may be atest sample as that term is defined herein. The glycosylated natriureticpeptides present in such a sample may be naturally present, such as in asample obtained from a patient, or may be a standard sample. Natriureticpeptides used in formulating such standards are often expressedrecombinantly in mammalian tissue culture systems, which contain activeglycosylation functions.

Following the deglycosylation step, the methods described herein mayemploy any assay methods known in the art. Such assay methods may employseparation methods such as affinity separation, gel electrophoresis,capillary electrophoresis, liquid chromatography, and/or HPLC toseparate analytes of interest for detection. In preferred embodiments,immunoassay devices and methods are often used for affinity separation,in various sandwich, competitive, or non-competitive assay formats, togenerate a signal that is related to the presence or amount of one ormore natriuretic peptides of interest. Additionally, certain methods anddevices, such as biosensors and optical immunoassays, may be employed todetermine the presence or amount of analytes without the need for alabeled molecule.

In addition, mass spectrometry methods may advantageously be employed aspart of the assay method. The terms “mass spectrometry” or “MS” as usedherein refer to methods of filtering, detecting, and measuring ionsbased on their mass-to-charge ratio, or “m/z.” In general, one or moremolecules of interest are ionized, and the ions are subsequentlyintroduced into a mass spectrographic instrument where, due to acombination of magnetic and electric fields, the ions follow a path inspace that is dependent upon mass (“m”) and charge (“z”). See, e.g.,U.S. Pat. No. 6,204,500, entitled “Mass Spectrometry From Surfaces;”U.S. Pat. No. 6,107,623, entitled “Methods and Apparatus for Tandem MassSpectrometry;” U.S. Pat. No. 6,268,144, entitled “DNA Diagnostics BasedOn Mass Spectrometry;” U.S. Pat. No. 6,124,137, entitled“Surface-Enhanced Photolabile Attachment And Release For Desorption AndDetection Of Analytes;” Wright et al., “Proteinchip surface enhancedlaser desorption/ionization (SELDI) mass spectrometry: a novel proteinbiochip technology for detection of prostate cancer biomarkers incomplex protein mixtures,” Prostate Cancer and Prostatic Diseases 2:264-76 (1999); and Merchant and Weinberger, “Recent advancements insurface-enhanced laser desorption/ionization-time of flight-massspectrometry,” Electrophoresis 21: 1164-67 (2000), each of which ishereby incorporated by reference in its entirety, including all tables,figures, and claims. Molecules (e.g., peptides) in a test sample can beionized by any method known to the skilled artisan. These methodsinclude, but are not limited to, electron ionization, chemicalionization, fast atom bombardment, field desorption, and matrix-assistedlaser desorption ionization (“MALDI”), surface enhanced laser desorptionionization (“SELDI”), photon ionization, electrospray, and inductivelycoupled plasma.

In certain embodiments, the MS methods discussed above are preferablycombined with an affinity purification step such as binding to anantibody that specifically binds one or more polypeptides of interest.See, e.g., Nelson et al., Anal. Chem., 67: 1153, 1995; Tubbs et al.,Anal. Biochem. 289: 26, 2001. Niederkofler et al., Anal. Chem. 73: 3294,2001.

One feature of glycoproteins is the typical heterogeneity of theglycans. It is very common for individual molecules of a givenglycoprotein to carry different carbohydrates at the same attachmentsite in the polypeptide chain. Any structural changes in thecarbohydrate residues will result in the formation of discrete molecularsubsets referred to as glycoforms. In the case of various separationmethods, such heterogeneity can substantially complicate the analysisdue to differences in charge and mass of the various polypeptides ofinterest and/or differences in the binding of the various polypeptidesof interest to a binding matrix (e.g., an antibody). In addition,carbohydrates are not ionized as efficiently as compounds such asproteins that can be easily protonated; neither do they appear to betransferred to the vapor phase as effectively.

Thus, in preferred embodiments, the methods described herein provide anincreased detection of one or more naturietic peptides of interest, ascompared to performing the same assaying step in the absence of removingone or more covalently bound carbohydrate residues from one or more ofthe natriuretic peptides of interest. The term “increased detection” asused herein refers to an increased signal obtained from the assay methodfor one or more particular naturietic peptides of interest. Such anincreased signal may be representative of an increased ability to detectall of the naturietic peptides of interest. For example, an antibodythat could not bind certain glycosylated forms of one or more naturieticpeptides of interest would result in an assay signal that underestimatesthe concentration of those naturietic peptides; or less efficientionization of certain glycosylated forms of one or more naturieticpeptides of interest would result in an assay signal by MS thatunderestimates the concentration of those naturietic peptides.Deglycosylation can result in an increased assay signal. Such anincreased signal may also be representative of an increased ability todetect one or more specific forms of the naturietic peptides ofinterest. For example, the heterogeneity of the glycans may result inseparation of a single polypeptide into a plurality of differentfractions in a separation method (e.g., those based on mass and/orcharge). Deglycosylation can result in coalescence of those differentfractions into a single fraction, thus providing an improved assaysignal for that fraction.

In various embodiments, the increased detection of one or morenaturietic peptides of interest, as compared to performing the sameassaying step in the absence of removing one or more covalently boundcarbohydrate residues from one or more of the natriuretic peptides ofinterest, is measured by an assay signal that increases by at leastabout 5%, more preferably at least about 10%, still more preferably atleast about 20%, even more preferably at least about 50%, still morepreferably at least about 100%, and most preferably at least about 200%or more.

In particularly preferred embodiments, the natriuretic peptides ofinterest are BNP and/or one or more of its related fragments. The term“related fragments” is defined hereinafter. Preferred BNP-relatedfragments comprise those selected from the group consisting of pro-BNP(BNP₁₋₁₀₈), NT-proBNP (BNP₁₋₇₆), BNP₃₋₁₀₈, BNP₃₋₇₆, and BNP₇₉₋₁₀₈. Thislist is not meant to be limiting.

In a related aspect, the present invention relates to methods forselecting and using antibodies that are either sensitive or insensitiveto the presence (or absence) of covalently bound carbohydrate residueson one or more natriuretic peptides of interest. Antibodies may bescreened for the ability to bind to one or more glycosylated natriureticpeptides of interest, and that binding may be compared to the ability tobind to one or more natriuretic peptides of interest following removalof one or more covalently bound carbohydrate residues. Those antibodiesthat provide substantially identical binding by this measure represent“insensitive” antibodies. Those antibodies that provide binding by thismeasure that is not substantially identical for glycosylated ordeglycosylated forms represent “sensitive” antibodies. Such antibodiesmay be selected for use in assay methods for the detection of one ormore natriuretic peptides of interest.

The term “removal of one or more covalently bound carbohydrate residues”in this context does not necessarily refer to the use of enzymatic ornon-enzymatic chemical treatments to remove existing carbohydrateresidues from a polypeptide. Instead, it is meant to encompass anymethod for generating a polypeptide lacking one or more covalently boundcarbohydrate residues. For example, solid phase synthesis methods may beused to generate a polypeptide that is free of all carbohydrate residuesfor use in such antibody screening methods. It is preferred that atleast about 50%, more preferably, at least about 60%, still morepreferably at least about 70%, yet more preferably at least about 80%,and most preferably at least about 90% to about 100% of the carbohydrateresidues are removed from one or more, and preferably all, of theglycosylated natriuretic peptides of interest for use in the screeningmethods described herein.

The term “substantially identical binding” refers to an antibody that,when used in an assay, provides signals that are within a factor ofabout 2 of one another in the screening comparison described above. Afactor of 1 indicates that the signals are equal; that signals arewithin a factor of 2 indicates that one signal is less than or equal tothe other signal x 2. Preferably, antibodies exhibiting substantiallyidentical binding provide signals that are within a factor of about1.75, more preferably within a factor of about 1.5, still morepreferably within a factor of about 1.25, and most preferably within afactor of about 1.1 to 1.

Such antibodies may also have “substantially identical affinity” for oneor more glycosylated natriuretic peptides of interest, as compared toone or more natriuretic peptides of interest following removal of one ormore covalently bound carbohydrate residues. A factor of 1 indicatesthat the affinities are equal; that affinities are within a factor of 2indicates that one affinity is less than or equal to the other signal x2. Preferably, antibodies exhibiting substantially identical bindingprovide affinities that are within a factor of about 1.75, morepreferably within a factor of about 1.5, still more preferably within afactor of about 1.25, and most preferably within a factor of about 1.1to 1.

The summary of the invention described above is non-limiting and otherfeatures and advantages of the invention will be apparent from thefollowing detailed description of the invention, and from the claims.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 shows a mass spectrum of BNP and its degradation products inhuman serum in the absence (panels A and C) and the presence (panels Band D) of an inhibitor of dipeptidyl peptidase.

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates in part to methods for distinguishingbetween biologically active (e.g., full length) natriuretic peptidesfrom biologically inactive forms of the natriuretic peptides. Asdescribed herein, antibodies may be generated that selectively recognizebiologically active natriuretic peptides, and used in assays thatexhibit reduced inaccuracies caused by the presence of inactivenatriuretic peptide fragments present in a sample.

The term “natriuretic peptide” as used herein refers to members of agroup of naturally occurring polypeptide hormones that act in the bodyto oppose the activity of the renin-angiotensin system, and theirbiosynthetic precursors and biologically active fragments. There arethree major human natriuretic peptides: atrial natriuretic peptide(ANP), which is synthesized in the atria; brain-type natriuretic peptide(BNP), which is synthesized in the ventricles; and C-type natriureticpeptide (CNP), which is synthesized in the brain.

The term “intact natriuretic peptide” as used herein refers to the fulllength pre-pro-natriuretic peptide, full length pro-natriuretic peptide,full length mature natriuretic peptide, and/or the full length portionsremoved during processing of the pre-pro- or pro-natriuretic peptidesduring biosynthesis. In the case of BNP for example, the term “intactnatriuretic peptides” encompasses the full length 32 amino acid matureBNP hormone; the full length 134-amino acid pre-pro-BNP molecule; thefull length 108-amino acid pro-BNP molecule; the full length 76-aminoacid NT-pro BNP molecule, and/or the full length 26-amino acid “pre”peptide.

The sequence of the human 108 amino acid BNP precursor pro-BNP(BNP₁₋₁₀₈) is shown as SEQ ID NO: 1. Mature, full length BNP (BNP₇₇₋₁₀₈)is shown underlined:

     (SEQ ID NO: 1)HPLGSPGSAS DLETSGLQEQ RNHLQGKLSE LQVEQTSLEP LQESPRPTGV    50WKSREVATEG IRGHRKMVLY TLRAPRSPKM VQGSGCFGRK MDRISSSSGL   100GCKVLRRH.                                                108

Human BNP₁₋₁₀₈ is synthesized as a larger precursor pre-pro-BNP havingthe sequence shown as SEQ ID NO: 2 (with the “pre” sequence shown inbold):

     (SEQ ID NO: 2)MDPQTAPSRA LLLLLFLHLA FLGGRSHPLG SPGSASDLET SGLQEQRNHL    50QGKLSELQVE QTSLEPLQES PRPTGVWKSR EVATEGIRGH RKMVLYTLRA   100PRSPKMVQGS GCFGRKMDRI SSSSGLGCKV LRRH.                   134

The sequence of the 126 amino acid human ANP precursor pro-ANP(ANP₁₋₁₂₆) is shown as SEQ ID NO: 3, with mature, full length ANP(ANP₉₉₋₁₂₆) underlined:

     (SEQ ID NO: 3)NPMYNAVSNA DLMDFKNLLD HLEEKMPLED EVVPPQVLSD PNEEAGAALS    50PLPEVPPWTG EVSPAQRDGG ALGRGPWDSS DRSALLKSKL RALLTAPRSL   100RRSSCFGGRM DRIGAQSGLG CNSFRY.                            126

Human ANP₁₋₁₂₆ is synthesized as a larger precursor pre-pro-ANP havingthe sequence shown in SEQ ID NO: 4 (with the “pre” sequence shown inbold):

     (SEQ ID NO: 4)MSSFSTTTVS FLLLLAFQLL GQTRANPMYN AVSNADLMDF KNLLDHLEEK    50MPLEDEVVPP QVLSDPNEEA GAALSPLPEV PPWTGEVSPA QRDGGALGRG   100PWDSSDRSAL LKSKLRALLT APRSLRRSSC FGGRMDRIGA QSGLGCNSFR   150Y.                                                       151

The sequence of the 126 amino acid human CNP precursor pro-CNP(CNP₁₋₁₂₆) is shown as SEQ ID NO: 5, with the full length mature CNPform CNP-53 (CNP₇₄₋₁₂₆) shown in italics, and the full length mature CNPform CNP-22 (CNP₁₀₅₋₁₂₆) shown underlined:

     (SEQ ID NO: 5)MHLSQLLACA LLLTLLSLRP SEAKPGAPPK VPRTPPAEEL AEPQAAGGGQ    50KKGDKAPGGG GANLKGDRSR LLRDLRVDTK SRAAWARLLQ EHPNARKYKG   100ANKKGLSKGC FGLKLDRIGS MSGLGC.                            126

The term “fragment” as used herein refers to a polypeptide thatcomprises at least six contiguous amino acids of a polypeptide fromwhich the fragment is derived, but is less than the complete parentpolypeptide. Thus, a fragment of pro-BNP (BNP₁₋₁₀₈) refers to apolypeptide that comprises at least six contiguous amino acids ofBNP₁₋₁₀₈; a fragment of mature BNP refers to a polypeptide thatcomprises at least six contiguous amino acids of BNP₇₇₋₁₀₈; a fragmentof the polypeptide generated by cleavage of pro-BNP into mature BNPrefers to a polypeptide that comprises at least six contiguous aminoacids of BNP₁₋₇₆. Similarly, a fragment of pro-ANP (ANP₁₋₁₂₆) refers toa polypeptide that comprises at least six contiguous amino acids ofANP₁₋₁₂₆; a fragment of mature ANP refers to a polypeptide thatcomprises at least six contiguous amino acids of ANP₉₉₋₁₂₆; a fragmentof the polypeptide generated by cleavage of pro-ANP into mature ANPrefers to a polypeptide that comprises at least six contiguous aminoacids of BNP₁₋₉₈; and a fragment of pro-CNP (CNP₁₋₁₂₆) refers to apolypeptide that comprises at least six contiguous amino acids ofCNP₁₋₁₂₆; a fragment of mature CNP refers to a polypeptide thatcomprises at least six contiguous amino acids of CNP₇₄₋₁₂₆ orCNP₁₀₅₋₁₂₆, a fragment of the polypeptide generated by cleavage ofpro-CNP into mature CNP refers to a polypeptide that comprises at leastsix contiguous amino acids of CNP₁₋₇₃ or CNP₁₋₁₀₄. In preferredembodiments, a fragment refers to a polypeptide that comprises at least10 contiguous amino acids of a polypeptide from which the fragment isderived; at least 15 contiguous amino acids of a polypeptide from whichthe fragment is derived; or at least 20 contiguous amino acids of apolypeptide from which the fragment is derived.

The term “related fragment” as used herein refers to one or morefragments of a particular polypeptide or its biosynthetic parent thatmay be detected as a surrogate for the polypeptide itself or asindependent markers. For example, human BNP is derived by proteolysis ofa 108 amino acid precursor molecule, referred to hereinafter asBNP₁₋₁₀₈. Mature SNP, or “the BNP natriuretic peptide,” or “BNP-32” is a32 amino acid molecule representing amino acids 77-108 of thisprecursor, which may be referred to as BNP₇₇₋₁₀₈. The remaining residues1-76 are referred to hereinafter as BNP₁₋₇₆. BNP₁₋₁₀₈ and BNP₁₋₇₆ areexamples of “BNP-related fragments.”

The term “fragment formed by removal of an N-terminal portion” as usedherein in reference to natriuretic peptide fragments refers to afragment of an intact natriuretic peptide formed by removal of one ormore amino acids from the amino terminal end of the intact peptide. Inpreferred embodiments, such a fragment is formed by removal of at least2, 3, 4, 5, 7, 10, 15, 20, or more amino acids from the amino terminalend of the intact peptide.

The term “biologically active” as used herein in reference tonatriuretic peptides and fragments thereof refers to a full lengthmature natriuretic peptide; or a polypeptide derived from the fulllength mature natriuretic peptide or its precursor molecules thatexhibit at least 50% of the vasorelaxation effects in isolatedpreconstricted mouse aortic rings exhibited by the full length maturenatriuretic peptide, measured as described in Lopez et al., J. Biol.Chem. 272: 23064-23068, 1997. Biologically active natriuretic peptidesmay include fragments of the full length mature natriuretic peptide, orprecursor forms or fragments thereof.

The term “biologically inactive” as used herein in reference tonatriuretic peptide fragments refers to a polypeptide derived from thefull length mature natriuretic peptide or its precursor that is not“biologically active” as defined above. As used herein, the term“biologically inactive” does not necessarily refer to a complete loss ofall biological activity. Rather, a “biologically inactive” natriureticpeptide fragment preferably exhibits less than 50%, preferably less than25%, more preferably less than 10%, and most preferably less than 1%, ofone or more biological functions of the intact natriuretic peptide. Thisbiological function may be receptor binding, which may be measured asdescribed in Smith et al., J. Endocrinal. 167: 23946, 2000, cGMPproduction in cultured rat aortic smooth muscle cells, which may bemeasured as described in Shimekake et al., FEBS Lett. 309: 185-9, 1992,and/or the vasorelaxation effects in isolated preconstricted mouseaortic rings exhibited by the full length mature natriuretic peptide,measured as described in Lopez et al., J Biol. Chem. 272: 23064-23068,1997, compared to that exhibited by the full length mature natriureticpeptide.

The term “glycosylated” as used herein in regard to polypeptides refersto polypeptides comprising covalently bound sugar units, often in theform of glycan chains. The individual sugar units are referred to hereinas “covalently bound carbohydrate residues.” Glycosylation ofpolypeptides in eukaryotics occurs principally through glycosidic bondsto an asparagine side chain (“N-linked”); through glycosidic bonds to toserine or threonine side chains (“O-linked”); or the polypeptide may belinked to a phosphatidylinositol lipid anchor through a carbohydratebridge (“GPI-linked”).

The term “deglycosylation” as used herein refers to methods for removingone or more covalently bound carbohydrate residues from polypeptides.While removal of all covalently bound carbohydrate residues ispreferred, a polypeptide is considered to have been deglycosylated ifany covalently bound carbohydrate residues have been removed. Enzymatictreatments, non-enzymatic treatments, or a combination of the two may beemployed to remove covalently bound carbohydrate residues frompolypeptides. It is preferred that at least about 50%, more preferably,at least about 60%, still more preferably at least about 70%, yet morepreferably at least about 80%, and most preferably at least about 90% toabout 100% of the carbohydrate residues are removed from a polypeptide.

As used herein, the term “purified” in reference to polypeptides doesnot require absolute purity. Instead, it represents an indication thatthe polypeptide(s) of interest is(are) in a discrete environment inwhich abundance (on a mass basis) relative to other proteins is greaterthan in a biological sample. By “discrete environment” is meant a singlemedium, such as a single solution, a single gel, a single precipitate,etc. Purified polypeptides may be obtained by a number of methodsincluding, for example, laboratory synthesis, chromatography,preparative electrophoresis, centrifugation, precipitation, affinitypurification, etc. One or more “purified” polypeptides of interest arepreferably at least 10% of the protein content of the discreteenvironment. One or more “substantially purified” polypeptides are atleast 50% of the protein content of the discrete environment, morepreferably at least 75% of the protein content of the discreteenvironment, and most preferably at least 95% of the protein content ofthe discrete environment. Protein content is determined using amodification of the method of Lowry et al., J. Biol. Chem. 193: 265,1951, described by Hartree, Anal Biochem 48: 422-427 (1972), usingbovine serum albumin as a protein standard.

The term “antibody” as used herein refers to a peptide or polypeptidederived from, modeled after or substantially encoded by animmunoglobulin gene or immunoglobulin genes, or fragments thereof,capable of specifically binding an antigen or epitope. See, e.g.Fundamental Immunology, P Edition, W. E. Paul, ed., Raven Press, N. Y.(1993); Wilson (1994) J. Immunol. Methods 175:267-273; Yarmush (1992) J.Biochem. Biophys. Methods 25:85-97. The term antibody includesantigen-binding portions, i.e., “antigen binding sites,” (e.g.,fragments, subsequences, complementarity determining regions (CDRs))that retain capacity to bind antigen, including (i) a Fab fragment, amonovalent fragment consisting of the VL, VH, CL and CH1 domains; (ii) aF(ab′)2 fragment, a bivalent fragment comprising two Fab fragmentslinked by a disulfide bridge at the hinge region; (iii) a Fd fragmentconsisting of the VH and CH1 domains; (iv) a Fv fragment consisting ofthe VL and VH domains of a single arm of an antibody, (v) a dAb fragment(Ward et al., (1989) Nature 341:544-546), which consists of a VH domain;and (vi) an isolated complementarity determining region (CDR). Singlechain antibodies, monoclonal antibodies, polyclonal antibodies, andantibodies obtained by molecular biological techniques (e.g., by phagedisplay methods) are also included by reference in the term “antibody.”Preferred antibodies are “Omniclonal” antibodies. By this is meant amixture of different antibody molecules selected from a phage displaylibrary, where each antibody specifically binds to a target antigen witha minimum affinity of 10⁹ M⁻¹ to 10¹ M⁻¹.

The term “specifically binds” is not intended to indicate that anantibody binds exclusively to its intended target. Rather, an antibody“specifically binds” if its affinity for its intended target is about5-fold greater when compared to its affinity for a non-target molecule.Preferably the affinity of the antibody will be at least about 5 fold,preferably 10 fold, more preferably 25-fold, even more preferably50-fold, and most preferably 100-fold or more, greater for a targetmolecule than its affinity for a non-target molecule. In preferredembodiments, Specific binding between an antibody or other binding agentand an antigen means a binding affinity of at least 10⁶ M⁻¹. Preferredantibodies bind with affinities of at least about 10⁷ M⁻¹, andpreferably between about 10⁸ M⁻¹ to about 10⁹ M⁻¹, about 10⁹ M⁻¹ toabout 10¹⁰ M⁻¹, or about 10¹⁰ M⁻¹ to about 10¹¹ M⁻¹.

Affinity is calculated as K_(d)=k_(off)/k^(on) (K_(off) is thedissociation rate constant, K_(on) is the association rate constant andK_(d) is the equilibrium constant. Affinity can be determined atequilibrium by measuring the fraction bound (r) of labeled ligand atvarious concentrations (c). The data are graphed using the Scatchardequation: r/c=K(n−r):

where

r=moles of bound ligand/mole of receptor at equilibrium;

c=free ligand concentration at equilibrium;

K=equilibrium association constant; and

n=number of ligand binding sites per receptor molecule

By graphical analysis, r/c is plotted on the Y-axis versus r on theX-axis thus producing a Scatchard plot. The affinity is the negativeslope of the line. k_(off) can be determined by competing bound labeledligand with unlabeled excess ligand (see, e.g., U.S. Pat. No.6,316,409). The affinity of a targeting agent for its target molecule ispreferably at least about 1×10⁻⁶ moles/liter, is more preferably atleast about 1×10⁻⁷ moles/liter, is even more preferably at least about1×10⁻⁸ moles/liter, is yet even more preferably at least about 1×10⁻⁹moles/liter, and is most preferably at least about 1×10⁻¹⁰ moles/liter.Antibody affinity measurement by Scatchard analysis is well known in theart. See, e.g., van Erp et al., J. Immunoassay 12: 425-43, 1991; Nelsonand Griswold, Comput. Methods Programs Biomed. 27: 65-8, 1988.

The term “discrete” as used herein refers to areas of a surface that arenon-contiguous. That is, two areas are discrete from one another if aborder that is not part of either area completely surrounds each of thetwo areas. The term “independently addressable” as used herein refers todiscrete areas of a surface from which a specific signal may beobtained. One skilled in the art will appreciate that antibody zones canalso be independent of each other, but can be in contact with each otheron a surface.

The term “test sample” as used herein refers to a sample in which thepresence or amount of one or more analytes of interest are unknown andto be determined in an assay, preferably an immunoassay. Preferably, atest sample is a bodily fluid obtained for the purpose of diagnosis,prognosis, or evaluation of a subject, such as a patient. In certainembodiments, such a sample may be obtained for the purpose ofdetermining the outcome of an ongoing condition or the effect of atreatment regimen on a condition. Preferred test samples include blood,serum, plasma, cerebrospinal fluid, urine and saliva. In addition, oneof skill in the art would realize that some test samples would be morereadily analyzed following a fractionation or purification procedure,for example, separation of whole blood into serum or plasma components.Preferred samples may be obtained from bacteria, viruses and animals,such as dogs and cats. Particularly preferred samples are obtained fromhumans. By way of contrast, a “standard sample” refers to a sample inwhich the presence or amount of one or more analytes of interest areknown prior to assay for the one or more analytes.

The term “disease sample” as used herein refers to a tissue sampleobtained from a subject that has been determined to suffer from a givendisease. Methods for clinical diagnosis are well known to those of skillin the art. See, e.g., Kelley's Textbook of Internal Medicine, 4th Ed.,Lippincott Williams & Wilkins, Philadelphia, Pa., 2000; The Merck Manualof Diagnosis and Therapy, 17^(th) Ed., Merck Research Laboratories,Whitehouse Station, N.J., 1999.

The terms “prolyl-specific dipeptidyl peptidase” or “prolyl-specificDPP” refer to serine proteases that cleave dipeptides from theN-terminal of substrate polypeptides, and that exhibit a preference forproline in the second position (i.e., NH2-X-pro-peptide-COOH, where X isan amino acid, and the bond between pro and the remaining peptide iscleaved). Such proteases are generally classified under E.C.3.4.14.X,including E.C.3.4.14.5 and 3.4.14.11. DPPs are often classified intotypes such as DPP-II and DPP-IV.

The term “inhibitor” as used herein in reference to molecules thataffect an enzymatic (e.g., proteolytic) activity does not necessarilyrefer to a complete loss of all enzymatic activity. Rather, an“inhibitor” reduces an enzymatic activity by at least 10%, morepreferably at least 25%, even more preferably by at least 50%, stillmore preferably by at least 75%, and most preferably by at least 90%, ofthe enzymatic activity exhibited in the absence of the inhibitor. Invitro, the activity of an inhibitor may be measured by directlymeasuring enzymatic activity by methods well known to those of skill inthe art. In vivo, the activity of an inhibitor may also be measured bydirectly measuring enzymatic activity on the enzyme substrate, or in thecase of a degradative enzyme, may be measured by determining a time(T_(1/2)) in which ½ of the substrate is cleared from the body of asubject (e.g., an experimental animal). In the latter case, an“inhibitor” increases a T_(1/2) by at least 10%, more preferably atleast 25%, even more preferably by at least 50%, still more preferablyby at least 75%, and most preferably by at least 90%, compared to theT_(1/2), exhibited in the absence of the inhibitor.

Preferred inhibitors are selective for a particular class of proteases(e.g., selective for dipeptidyl peptidase or for a particular subset ofdipeptidyl peptidase). An inhibitor is said to be “selective” for aparticular class of protease if it inhibits that class at least 10-foldmore, more preferably at least 100-fold more, and most preferably atleast 1000-fold more, than non-target proteases. Selective inhibitors ofvarious DPP types are known. For example, H-Dab-Pip is reportedly beselective (>7,600-fold) for dipeptidyl peptidase II (DPP II; EC3.4.14.2) over DPP IV (IC₅₀>1 mM) (DPP IV; EC 3.4.14.5). Senten et al.,Bioorg. Med. Chem. Lett. 12: 2825, 2002. Similarly,1-[[[2-[(5-cyanopyridin-2-yl)amino]ethyl]amino]acetyl]-2-cyano-(S)-pynrolidineis reportedly a selective, orally active inhibitor of DPP IV. Ahren etal., Diabetes Care 25:869-75, 2002.

The term “about” as used herein refers to +/−10% of a given number.

Use of Natriuretic Peptide Fragments as Prognostic and DiagnosticMarkers

As noted above, increased blood levels of natriuretic peptides have beenfound in certain disease states, suggesting a role in thepathophysiology of those diseases, including stroke, congestive heartfailure (CHF), cardiac ischemia, systemic hypertension, and acutemyocardial infarction. See, e.g., WO 02/089657; WO 02/083913; WO03/016910; Hunt et al., Biochem. Biophys. Res. Comm. 214: 1175-83(1995); Venugopal, J. Clin. Pharm. Ther. 26: 1531, 2001; and Kalra etal., Circulation 107: 571-3, 2003; each of which is hereby incorporatedin its entirety, including all tables, figures, and claims. Thenatriuretic peptides, alone, collectively, and/or together withadditional proteins, can also serve as disease markers and indicators ofprognosis in various cardiovascular conditions.

It has been reported that removal of natriuretic peptides from thecirculation involves degradation pathways. Indeed, inhibitors of neutralendopeptidase, which cleaves natriuretic peptides under certaincircumstances, have been suggested to hold promise in treatment ofcertain cardiovascular diseases. See, e.g., Trindade and Rouleau, HeartFail. Monit. 2: 2-7, 2001. However, the measurement of the natriureticpeptides in clinical samples has focused generally upon measurement ofBNP, ANP, and/or CNP; their precursor molecules (i.e., pro-BNP, pro-ANP,and pro-CNP); and the fragments resulting from cleavage of the pro-formto provide the mature natriuretic peptides, without consideration of thedegradation state of the molecules. It has also been reported thatoxidation of methionine residues in the natriuretic peptides reduces thebiological activity compared to reduced forms. Koyama et al., Eur. J.Biochem. 203: 425-32. For the purposes described herein, themethionine-oxidized forms may be considered products of degradation.

The present invention describes for the first time that assays whichhave not been designed with an understanding of the degradation pathwaysof the natriuretic peptides and the products formed during thisdegradation, may not accurately measure the biologically active forms ofa particular natriuretic peptide in a sample. The unintended measurementof both the biologically active natriuretic peptide(s) of interest andinactive fragments derived from the natriuretic peptide may result in anoverestimation of the concentration of biologically active natriureticpeptide(s) in a sample. While described hereinafter mainly withreference to BNP-related fragments, the skilled artisan will understandthat the general concepts described herein apply equally to ANP- andCNP-related fragments.

The failure to consider the activity of the various natriuretic peptidesand their fragments that may be present in a clinical sample whenmeasuring one or more of the natriuretic peptides may have seriousconsequences for the accuracy of any diagnostic or prognostic method.Consider for example a simple case, where a sandwich immunoassay isprovided for BNP, and a significant amount (e.g., 50%) of thebiologically active BNP that had been present has now been degraded intoan inactive form. An immunoassay formulated with antibodies that bind aregion common to the biologically active BNP and the inactivefragment(s) will overestimate the amount of biologically active BNPpresent in the sample by 2-fold, potentially resulting in a “falsepositive” result. This inaccuracy may be particularly relevant in thecase of severe heart failure, as neutral endopeptidase expression hasbeen reported to be increased in these patients. Knecht et al., LifeSci. 71: 2701-12, 2002. This increased expression of the enzyme believedresponsible for natriuretic peptide degradation could be expected toincrease the inactive fragment pool in these patients.

Overestimation of the natriuretic peptide concentration of a sample mayalso have serious consequences for patient management. For example, BNPconcentration may be used to determine if therapy for congestive heartfailure is effective (e.g., by monitoring BNP to see if an elevatedlevel is returning to normal upon treatment). The same “false positive”BNP result discussed above may lead the physician to continue, increase,or modify treatment (e.g., increase the dosage of diuretic, ACEinhibitor, digoxin, (3-blocker, calcium channel blocker, and/orvasodilator, or even consider surgical intervention) because of thefalse impression that current therapy is ineffective.

Similarly, the present invention describes that assays that have notbeen designed with an understanding of the glycosylation state of thenatriuretic peptides may likewise not accurately measure the forms of aparticular natriuretic peptide in a sample. Antibodies are often raisedfor use in assays through the use of synthetic peptides or expressedpeptides that lack the natural glycosylation profile seen in vivo.Consider for example a simple case, where a sandwich immunoassay isprovided for BNP, and a significant amount (e.g., 50%) of the BNPpresent has glycosylation that interferes with antibody binding. Animmunoassay formulated with such antibodies will underestimate theamount of BNP present in the sample by 2-fold, potentially resulting ina “false negative” result.

Glycosylation differences amongst the natriuretic peptides may alsoresult in differences in biological activity, either through differencesin activity at the natriuretic peptide receptor or through differencesin biological half-life due to the glycosylation state of a particularnatriuretic peptide. Thus, the methods herein may also be used togenerate assays that are specific for certain glycosylation states,again to improve the accuracy of diagnostic and therapeutic utility ofsuch assays.

The skilled artisan will understand that the methods described hereinare applicable generally to polypeptides, and the analysis of thenatriuretic peptides described in detail herein is merely exemplary.Other suitable polypeptides that may be the subject of similar analysisinclude angiotensin I, angiotensin II, vasopressin, calcitonin,calcitonin gene related peptide, urodilatin, urotensin II, free cardiactroponin I, free cardiac troponin T, cardiac troponin I in a complexcomprising one or both of troponin T and troponin C, cardiac troponin Tin a complex comprising one or both of troponin I and troponin C, totalcardiac troponin I, total cardiac troponin T, pulmonary surfactantprotein D, D-dimer, annexin V, enolase, creatine kinase, glycogenphosphorylase, heart-type fatty acid binding protein, phosphoglycericacid mutase, S-100, S-100ao, plasmin-α2-antiplasmin complex,β-thromboglobulin, platelet factor 4, fibrinopeptide A, platelet-derivedgrowth factor, prothrombin fragment 1+2, P-selectin,thrombin-antithrombin III complex, von Willebrand factor, tissue factor,thrombus precursor protein, human neutrophil elastase, inducible nitricoxide synthase, lysophosphatidic acid, malondialdehyde-modified lowdensity lipoprotein, matrix metalloproteinase-1, matrixmetalloproteinase-2, matrix metalloproteinase-3, matrixmetalloproteinase-9, TIMP1, TIMP2, TIMP3, C-reactive protein,interleukin-1β, interleukin-1 receptor antagonist, interleukin-6, tumornecrosis factor α, soluble intercellular adhesion molecule-1, vascularcell adhesion molecule, monocyte chemotactic protein-1, caspase-3, humanlipocalin-type prostaglandin D synthase, mast cell tryptase, eosinophilcationic protein, KL-6, procalcitonin, haptoglobin, s-CD40 ligand, S-FASligand, alpha 2 actin, basic calponin 1, CSRP2 elastin, LTBP4, smoothmuscle myosin, smooth muscle myosin heavy chain, transgelin,aldosterone, angiotensin III, bradykinin, endothelin 1, endotehlin 2,endothelin 3, renin, APO B48, pancreatic elastase 1, pancreatic lipase,sPLA2, trypsinogen activation peptide, alpha enolase, LAMP3,phospholipase D, PLA2G5, protein D, SFTPC, defensin HBD1, defensin HBD2,CXCL-1, CXCL-2, CXCL-3, CCL2, CCL3, CCL4, CCL8, procalcitonin, proteinC, serum amyloid A, s-glutathione, s-TNF P55, s-TNF P75, TAFI, TGF beta,MMP-11, brain fatty acid binding protein, CA11, CABP1, CACNA1A, CBLN1,CHN2, cleaved Tau, CRHR1, DRPLA, EGF, GPM6B, GPR7, GPR8, GRIN2C, GRM7,HAPIP, HIF 1 alpha, HIP2 KCNK4, KCNK9, KCNQ5, MAPK10, n-acetylaspartate, NEUROD2, NRG2, PACE4, phosphoglycerate mutase, PKC gamma,prostaglandin E2, PTEN, PTPRZ1, RGS9, SCAT, secretagogin, SLC1A3, SORL1,SREB3, STAC, STX1A, STXBP 1, BDNF, cystatin C, neurokinin A, substanceP, interleukin-1, interleukin-11, interleukin-13, interleukin-18,interleukin-4, and interleukin-10.

Glycosylation of Natriuretic Peptides

Glycosylated polypeptides typically comprise N-linked sugars attached tothe amino group of one or more asparagine residues; O-linked sugarsattached to the hydroxyl group of one or more serine and/or threonineresidues; or a combination of N- and O-linked sugars. The presentinvention demonstrates for the first time that natriuretic peptides areglycosylated. Furthermore, the present invention demonstrates thatglycosylation can significantly affect the ability of certain methods ofdetecting natriuretic peptides in samples.

Several approaches may be used to obviate the potential difficultiespresented by glycosylation to a detection scheme. First, one may usechemical or enzymatic treatments to remove carbohydrate residues fromthe polypeptides, thereby shifting one or more of the naturieticpeptides of interest to a “detectable” state if the presence ofglycosylation disrupting accurate detection. Second, one may carefullyselect antibodies that bind to one or more regions of the naturieticpeptides of interest that are not subject to interference byglycosylation to provide antibodies that are “insensitive” to aparticular glycosylation state. Third, one may carefully selectantibodies that bind to one or more regions of the naturietic peptidesof interest that are glycosylated, but that exhibit reduced binding inthe deglycosylated state, to provide antibodies that are “sensitive” toa particular glycosylation state. Fourth, one may carefully selectantibodies that bind to one or more regions of the naturietic peptidesof interest that are glycosylated, but that exhibit increased binding inthe deglycosylated state, to provide antibodies that are “sensitive” toa particular glycosylation state. One may also combine these approachesas necessary or desired.

Effective enzymatic methods for removing N- and O-linked carbohydrateresidues are well known in the art, using enzymes such as N-glycanase(also known as N-glycosidase), endoglycosidase H, endoglycosidase A,0-glycanase (also known as endo-α-N-acetylgalactosaminidase),α2-(3,6,8,9)-neuriminidase, β(1,4)-galactosidase,N-acetylglucosaminidase, endoglycosidase F₁, endoglycosidase F₂, and/orendoglycosidase F₃. This list is not meant to be limiting. Suchenzymatic methods of sugar removal from peptides may be used on native(non-denatured) peptides. In such enzymatic methods, however,denaturation of the glycopeptide may be employed, often with anincreased rate of deglycosylation. Common denaturation conditionscomprise the addition of about 0.01% to about 1% sodium dodecyl sulfate(“SDS”), and optionally about 5 mM to about 500 mM β-mercaptoethanol, ina buffer solution at about neutral pH (i.e., between about pH 6.5 andabout pH 8). Such methods may further comprise from about 0.2% to about2% NP-40, which can serve to stabilize some deglycosylation enzymes.Increased temperature (e.g., about 37° C. for from about 0.5 hours toabout 48 hours) may also be employed together with such denaturationconditions.

In the case of non-enzymatic chemical treatments for removal ofcovalently bound carbohydrate residues from peptides, hydrazinehydrolysis has been found to be effective in the release of unreduced O-and N-linked oligosaccharides. Selective and sequential release ofoligosaccharides can be accomplished by initial mild hydrazinolysis ofthe O-linked oligosaccharides at about 60° C. followed by N-linkedoligosaccharides at about 95° C. See, e.g., Patel and Rarekh, Meth.Enzymol. 230, 58-66, 1994. Such treatment may result in destruction ofthe polypeptide however. Alkaline-β-elimination of O-linkedoligosaccharides, which utilizes alkaline sodium borohydride in a mildbase environment, may be preferred. See, e.g., Glycobiology: A PracticalApproach, Fukuda, M. and Kobata, A. (Eds), pp. 291-328, IRL/Oxford Univ.Press, Oxford, 1993. In addition, trifluoromethanesulfonic acidhydrolysis may be employed. This method typically leaves an intactpolypeptide, but results in destruction of the glycan, as glycosyllinkages between sugars are sensitive to cleavage bytrifluoromethanesulfonic acid, but peptide bonds are stable to evenprolonged treatment. See, e.g., Edge, Biochem. J. 376: 339-50, 2003.

Importantly, changes in mass observed in peptides following suchenzymatic or trifluoromethanesulfonic acid treatment can be ascribed toremoval of sugar residues, as post-translational modifications otherthan glycosylation are believed to be stable to such treatments. Thiscan allow for better understanding of the relative contribution ofcarbohydrates and glycosylation sites to the antigenic epitopes on thepolypeptides of interest. Deglycoylation can also allow betterunderstanding of differences in polypeptide mass (e.g., the mass of thenatriuretic peptides of interest and fragments thereof present in asample, which can be related by methods well known to those of skill inthe art to the sequence), as the removal of sugar residues removes anydoubt as to whether differences in mass observed may be due todifferences in sugar content rather than amino acid content.

Selection of Antibodies

The generation and selection of antibodies that preferentially recognizeintact natriuretic peptides fragments and/or are sensitive orinsensitive to glycosylation state may be accomplished several ways. Forexample, one way is to purify fragments or to synthesize the fragmentsof interest using, e.g., solid phase peptide synthesis methods wellknown in the art. See, e.g., Guide to Protein Purification, Murray P.Deutcher, ed., Meth. Enzymol. Vol 182 (1990); Solid Phase PeptideSynthesis, Greg B. Fields ed., Meth. Enzymol. Vol 289 (1997); Kiso etal., Chem. Pharm. Bull. (Tokyo) 38: 1192-99, 1990; Mostafavi et al.,Biomed. Pept. Proteins Nucleic Acids 1: 255-60, 1995; Fujiwara et al.,Chem. Pharm. Bull. (Tokyo) 44: 1326-31, 1996. The selected polypeptidesmay then be injected, for example, into mice or rabbits, to generatepolyclonal or monoclonal antibodies. One skilled in the art willrecognize that many procedures are available for the production ofantibodies, for example, as described in Antibodies, A LaboratoryManual, Ed Harlow and David Lane, Cold Spring Harbor Laboratory (1988),Cold Spring Harbor, N.Y. One skilled in the art will also appreciatethat binding fragments or Fab fragments which mimic antibodies can alsobe prepared from genetic information by various procedures (AntibodyEngineering: A Practical Approach (Borrebaeck, C., ed.), 1995, OxfordUniversity Press, Oxford; J. Immunol. 149, 3914-3920 (1992)).

In addition, numerous publications have reported the use of phagedisplay technology to produce and screen libraries of polypeptides forbinding to a selected target. See, e.g., Cwirla et al., Proc. Natl.Acad. Sci. USA 87, 6378-82, 1990; Devlin et al., Science 249, 404-6,1990, Scott and Smith, Science 249, 386-88, 1990; and Ladner et al.,U.S. Pat. No. 5,571,698. A basic concept of phage display methods is theestablishment of a physical association between DNA encoding apolypeptide to be screened and the polypeptide. This physicalassociation is provided by the phage particle, which displays apolypeptide as part of a capsid enclosing the phage genome which encodesthe polypeptide. The establishment of a physical association betweenpolypeptides and their genetic material allows simultaneous massscreening of very large numbers of phage bearing different polypeptides.Phage displaying a polypeptide with affinity to a target bind to thetarget and these phage are enriched by affinity screening to the target.The identity of polypeptides displayed from these phage can bedetermined from their respective genomes. Using these methods apolypeptide identified as having a binding affinity for a desired targetcan then be synthesized in bulk by conventional means. See, e.g., U.S.Pat. No. 6,057,098, which is hereby incorporated in its entirety,including all tables, figures, and claims.

The antibodies that are generated by these methods may then be selectedby first screening for affinity and specificity with the purified intactnatriuretic peptide of interest and, if required, comparing the resultsto the affinity and specificity of the antibodies with natriureticfragments that are desired to be excluded from binding. The screeningprocedure can involve immobilization of the purified natriureticfragments in separate wells of microtiter plates. The solutioncontaining a potential antibody or groups of antibodies is then placedinto the respective microtiter wells and incubated for about 30 min to 2h. The microtiter wells are then washed and a labeled secondary antibody(for example, an anti-mouse antibody conjugated to alkaline phosphataseif the raised antibodies are mouse antibodies) is added to the wells andincubated for about 30 min and then washed. Substrate is added to thewells and a color reaction will appear where antibody to the immobilizednatriuretic peptide(s) and fragments) are present. A similar approachmay be used to screen glycosylation-insensitive antibodies. In thiscase, screening may take place using purified natriuretic fragmentscontaining and lacking one or more carbohydrate residues.

The antibodies so identified may then be further analyzed for affinityand specificity to the natriuretic peptide(s) of interest in the assaydesign selected. In the development of immunoassays for a targetprotein, the purified target protein acts as a standard with which tojudge the sensitivity and specificity of the immunoassay using theantibodies that have been selected. Because the binding affinity ofvarious antibodies may differ; certain antibody pairs (e.g., in sandwichassays) may interfere with one another sterically, etc., assayperformance of an antibody may be a more important measure than absoluteaffinity and specificity of an antibody.

Those skilled in the art will recognize that many approaches can betaken in producing antibodies or binding fragments and screening andselecting for affinity and specificity for the various natriureticpeptides, but these approaches do not change the scope of the invention.

Use of Natriuretic Peptides in Marker Panels

Methods and systems for the identification of one or more markers forthe diagnosis, and in particular for the differential diagnosis, ofdisease have been described previously. Suitable methods for identifyingmarkers useful for the diagnosis of disease states are described indetail in U.S. patent application Ser. No. 10/331,127, entitled Methodand System for Disease Detection using Marker Combinations (attorneydocket no. 071949-6802), filed Dec. 27, 2002, which is herebyincorporated by reference in its entirety, including all tables,figures, and claims. One skilled in the art will also recognize thatunivariate analysis of markers can be performed and the data from theunivariate analyses of multiple markers can be combined to form panelsof markers to differentiate different disease conditions.

In developing a panel of markers useful in diagnosis, data for a numberof potential markers may be obtained from a group of subjects by testingfor the presence or level of certain markers. The group of subjects isdivided into two sets, and preferably the first set and the second seteach have an approximately equal number of subjects. The first setincludes subjects who have been confirmed as having a disease or, moregenerally, being in a first condition state. For example, this first setof patients may be those that have recently had a disease incidence, ormay be those having a specific type of disease. The confirmation of thecondition state may be made through a more rigorous and/or expensivetesting such as MRI or CT. Hereinafter, subjects in this first set willbe referred to as “diseased”.

The second set of subjects is simply those who do not fall within thefirst set. Subjects in this second set may be “non-diseased;” that is,normal subjects. Alternatively, subjects in this second set may beselected to exhibit one symptom or a constellation of symptoms thatmimic those symptoms exhibited by the “diseased” subjects. In stillanother alternative, this second set may represent those at a differenttime point from disease incidence.

The data obtained from subjects in these sets includes levels of aplurality of markers, including for purposes of the present invention,one or more fragments of natriuretic peptides either measuredindividually or as a group. Preferably, data for the same set of markersis available for each patient. This set of markers may include allcandidate markers which may be suspected as being relevant to thedetection of a particular disease or condition. Actual known relevanceis not required. Embodiments of the methods and systems described hereinmay be used to determine which of the candidate markers are mostrelevant to the diagnosis of the disease or condition. The levels ofeach marker in the two sets of subjects may be distributed across abroad range, e.g., as a Gaussian distribution. However, no distributionfit is required.

A marker often is incapable of definitively identifying a patient aseither diseased or non-diseased. For example, if a patient is measuredas having a marker level that falls within the overlapping region, theresults of the test will be useless in diagnosing the patient. Anartificial cutoff may be used to distinguish between a positive and anegative test result for the detection of the disease or condition.Regardless of where the cutoff is selected, the effectiveness of thesingle marker as a diagnosis tool is unaffected. Changing the cutoffmerely trades off between the number of false positives and the numberof false negatives resulting from the use of the single marker. Theeffectiveness of a test having such an overlap is often expressed usinga ROC (Receiver Operating Characteristic) curve. ROC curves are wellknown to those skilled in the art.

The horizontal axis of the ROC curve represents (1-specificity), whichincreases with the rate of false positives. The vertical axis of thecurve represents sensitivity, which increases with the rate of truepositives. Thus, for a particular cutoff selected, the value of(1-specificity) may be determined, and a corresponding sensitivity maybe obtained. The area under the ROC curve is a measure of theprobability that the measured marker level will allow correctidentification of a disease or condition. Thus, the area under the ROCcurve can be used to determine the effectiveness of the test.

As discussed above, the measurement of the level of a single marker mayhave limited usefulness. The measurement of additional markers providesadditional information, but the difficulty lies in properly combiningthe levels of two potentially unrelated measurements. In the methods andsystems according to embodiments of the present invention, data relatingto levels of various markers for the sets of diseased and non-diseasedpatients may be used to develop a panel of markers to provide a usefulpanel response. The data may be provided in a database such as MicrosoftAccess, Oracle, other SQL databases or simply in a data file. Thedatabase or data file may contain, for example, a patient identifiersuch as a name or number, the levels of the various markers present, andwhether the patient is diseased or non-diseased.

Next, an artificial cutoff region may be initially selected for eachmarker. The location of the cutoff region may initially be selected atany point, but the selection may affect the optimization processdescribed below. In this regard, selection near a suspected optimallocation may facilitate faster convergence of the optimizer. In apreferred method, the cutoff region is initially centered about thecenter of the overlap region of the two sets of patients. In oneembodiment, the cutoff region may simply be a cutoff point. In otherembodiments, the cutoff region may have a length of greater than zero.In this regard, the cutoff region may be defined by a center value and amagnitude of length. In practice, the initial selection of the limits ofthe cutoff region may be determined according to a pre-selectedpercentile of each set of subjects. For example, a point above which apre-selected percentile of diseased patients are measured may be used asthe right (upper) end of the cutoff range.

Each marker value for each patient may then be mapped to an indicator.The indicator is assigned one value below the cutoff region and anothervalue above the cutoff region. For example, if a marker generally has alower value for non-diseased patients and a higher value for diseasedpatients, a zero indicator will be assigned to a low value for aparticular marker, indicating a potentially low likelihood of a positivediagnosis. In other embodiments, the indicator may be calculated basedon a polynomial. The coefficients of the polynomial may be determinedbased on the distributions of the marker values among the diseased andnon-diseased subjects.

The relative importance of the various markers may be indicated by aweighting factor. The weighting factor may initially be assigned as acoefficient for each marker. As with the cutoff region, the initialselection of the weighting factor may be selected at any acceptablevalue, but the selection may affect the optimization process. In thisregard, selection near a suspected optimal location may facilitatefaster convergence of the optimizer. In a preferred method, acceptableweighting coefficients may range between zero and one, and an initialweighting coefficient for each marker may be assigned as 0.5. In apreferred embodiment, the initial weighting coefficient for each markermay be associated with the effectiveness of that marker by itself. Forexample, a ROC curve may be generated for the single marker, and thearea under the ROC curve may be used as the initial weightingcoefficient for that marker.

Next, a panel response may be calculated for each subject in each of thetwo sets. The panel response is a function of the indicators to whicheach marker level is mapped and the weighting coefficients for eachmarker. In a preferred embodiment, the panel response (R) for a eachsubject (j) is expressed as:

R _(j) =Σw _(i) I _(i,j),

where i is the marker index, j is the subject index, w_(i) is theweighting coefficient for marker i, I is the indicator value to whichthe marker level for marker i is mapped for subject j, and Σ is thesummation over all candidate markers i.

One advantage of using an indicator value rather than the marker valueis that an extraordinarily high or low marker levels do not change theprobability of a diagnosis of diseased or non-diseased for thatparticular marker. Typically, a marker value above a certain levelgenerally indicates a certain condition state. Marker values above thatlevel indicate the condition state with the same certainty. Thus, anextraordinarily high marker value may not indicate an extraordinarilyhigh probability of that condition state. The use of an indicator whichis constant on one side of the cutoff region eliminates this concern.

The panel response may also be a general function of several parametersincluding the marker levels and other factors including, for example,race and gender of the patient. Other factors contributing to the panelresponse may include the slope of the value of a particular marker overtime. For example, a patient may be measured when first arriving at thehospital for a particular marker. The same marker may be measured againan hour later, and the level of change may be reflected in the panelresponse. Further, additional markers may be derived from other markersand may contribute to the value of the panel response. For example, theratio of values of two markers may be a factor in calculating the panelresponse.

Having obtained panel responses for each subject in each set ofsubjects, the distribution of the panel responses for each set may nowbe analyzed. An objective function may be defined to facilitate theselection of an effective panel. The objective function should generallybe indicative of the effectiveness of the panel, as may be expressed by,for example, overlap of the panel responses of the diseased set ofsubjects and the panel responses of the non-diseased set of subjects. Inthis manner, the objective function may be optimized to maximize theeffectiveness of the panel by, for example, minimizing the overlap.

In a preferred embodiment, the ROC curve representing the panelresponses of the two sets of subjects may be used to define theobjective function. For example, the objective function may reflect thearea under the ROC curve. By maximizing the area under the curve, onemay maximize the effectiveness of the panel of markers. In otherembodiments, other features of the ROC curve may be used to define theobjective function. For example, the point at which the slope of the ROCcurve is equal to one may be a useful feature. In other embodiments, thepoint at which the product of sensitivity and specificity is a maximum,sometimes referred to as the “knee,” may be used. In an embodiment, thesensitivity at the knee may be maximized. In further embodiments, thesensitivity at a predetermined specificity level may be used to definethe objective function. Other embodiments may use the specificity at apredetermined sensitivity level may be used. In still other embodiments,combinations of two or more of these ROC-curve features may be used.

It is possible that one of the markers in the panel is specific to thedisease or condition being diagnosed. When such markers are present atabove or below a certain threshold, the panel response may be set toreturn a “positive” test result. When the threshold is not satisfied,however, the levels of the marker may nevertheless be used as possiblecontributors to the objective function.

An optimization algorithm may be used to maximize or minimize theobjective function. Optimization algorithms are well-known to thoseskilled in the art and include several commonly available minimizing ormaximizing functions including the Simplex method and other constrainedoptimization techniques. It is understood by those skilled in the artthat some minimization functions are better than others at searching forglobal minimums, rather than local minimums. In the optimizationprocess, the location and size of the cutoff region for each marker maybe allowed to vary to provide at least two degrees of freedom permarker. Such variable parameters are referred to herein as independentvariables. In a preferred embodiment, the weighting coefficient for eachmarker is also allowed to vary across iterations of the optimizationalgorithm. In various embodiments, any permutation of these parametersmay be used as independent variables.

In addition to the above-described parameters, the sense of each markermay also be used as an independent variable. For example, in many cases,it may not be known whether a higher level for a certain marker isgenerally indicative of a diseased state or a non-diseased state. Insuch a case, it may be useful to allow the optimization process tosearch on both sides. In practice, this may be implemented in severalways. For example, in one embodiment, the sense may be a truly separateindependent variable which may be flipped between positive and negativeby the optimization process. Alternatively, the sense may be implementedby allowing the weighting coefficient to be negative.

The optimization algorithm may be provided with certain constraints aswell. For example, the resulting ROC curve may be constrained to providean area-under-curve of greater than a particular value. ROC curveshaving an area under the curve of 0.5 indicate complete randomness,while an area under the curve of 1.0 reflects perfect separation of thetwo sets. Thus, a minimum acceptable value, such as 0.75, may be used asa constraint, particularly if the objective function does notincorporate the area under the curve. Other constraints may includelimitations on the weighting coefficients of particular markers.Additional constraints may limit the sum of all the weightingcoefficients to a particular value, such as 1.0.

The iterations of the optimization algorithm generally vary theindependent parameters to satisfy the constraints while minimizing ormaximizing the objective function. The number of iterations may belimited in the optimization process. Further, the optimization processmay be terminated when the difference in the objective function betweentwo consecutive iterations is below a predetermined threshold, therebyindicating that the optimization algorithm has reached a region of alocal minimum or a maximum.

Thus, the optimization process may provide a panel of markers includingweighting coefficients for each marker and cutoff regions for themapping of marker values to indicators. In order to develop lower-costpanels which require the measurement of fewer marker levels, certainmarkers may be eliminated from the panel. In this regard, the effectivecontribution of each marker in the panel may be determined to identifythe relative importance of the markers. In one embodiment, the weightingcoefficients resulting from the optimization process may be used todetermine the relative importance of each marker. The markers with thelowest coefficients may be eliminated.

In certain cases, the lower weighting coefficients may not be indicativeof a low importance. Similarly, a higher weighting coefficient may notbe indicative of a high importance. For example, the optimizationprocess may result in a high coefficient if the associated marker isirrelevant to the diagnosis. In this instance, there may not be anyadvantage that will drive the coefficient lower. Varying thiscoefficient may not affect the value of the objective function.

Use of Natriuretic Peptides for Determining a Treatment Regimen

A useful diagnostic or prognostic indicator such as the natriureticpeptides can help clinicians select between alternative therapeuticregimens. For example, patients with elevation in cardiac troponin T orI following an acute coronary syndrome appear to derive specific benefitfrom an early aggressive strategy that includes potent antiplatelet andantithrombotic therapy, and early revascularization. Hamm et al., N.Engl. J. Med. 340: 1623-9 (1999); Morrow et al., J. Am. Coll. Cardiol.36: 1812-7 (2000); Cannon et al., Am. J. Cardiol. 82: 731-6 (1998).Additionally, patients with elevation in C-reactive protein followingmyocardial infarction appear to derive particular benefit from HMG-CoAReductase Inhibitor therapy. Ridker et al., Circulation 98: 839-44(1998). Among patients with congestive heart failure, pilot studiessuggest that ACE inhibitors may reduce BNP levels in a dose dependentmanner. Van Veldhuisen et al., J. Am. Coll. Cardiol. 32: 1811-8 (1998).

Similarly, “tailoring” diuretic and vasodilator therapy based on thelevel of the biologically active natriuretic peptides may improveoutcomes. See, e.g., Troughton et al., Lancet 355: 1126-30 (2000).Finally, in a single pilot study of 16 patients found that randomizationto an ACE inhibitor rather than placebo following Q-wave MI wasassociated with reduced BNP levels over the subsequent 6-month period.Motwani et al., Lancet 341: 1109-13 (1993). Because BNP is acounter-regulatory hormone with beneficial cardiac and renal effects, itis likely that a change in BNP concentration reflects improvedventricular function and reduced ventricular wall stress. A recentarticle demonstrates the correlation of NT pro-BNP and BNP assays(Fischer et al., Clin. Chem. 47: 591-594 (2001). It is a furtherobjective of this invention that the concentration of natriureticpeptides, either individually or considered in groups of markers, can beused to guide diuretic and vasodilator therapy to improve patientoutcome. Additionally, the measurement of natriuretic peptides, eitherindividually or considered in groups of markers, for use as a prognosticindicator for patients is within the scope of the present invention.

Recent studies in patients hospitalized with congestive heart failuresuggest that serial BNP measurements may provide incremental prognositicinformation as compared to a single measurement; that is, assays candemonstrate an improving prognosis when BNP falls after therapy thanwhen it remains persistently elevated. Cheng et al., J. Am. Coll.Cardiol. 37: 386-91 (2001). Thus, serial measurements of natriureticpeptides according to the present invention may increase the prognosticand/or diagnostic value of a marker in patients, and is thus within thescope of the present invention.

Assay Measurement Strategies

Numerous methods and devices are well known to the skilled artisan forthe detection and analysis of polypeptides or proteins in test samples.In preferred embodiments, immunoassay devices and methods are oftenused. See, e.g., U.S. Pat. Nos. 6,143,576; 6,113,855; 6,019,944;5,985,579; 5,947,124; 5,939,272; 5,922,615; 5,885,527; 5,851,776;5,824,799; 5,679,526; 5,525,524; and 5,480,792, each of which is herebyincorporated by reference in its entirety, including all tables, figuresand claims. These devices and methods can utilize labeled molecules invarious sandwich, competitive, or non-competitive assay formats, togenerate a signal that is related to the presence or amount of ananalyte of interest. Additionally, certain methods and devices, such asbiosensors and optical immunoassays, may be employed to determine thepresence or amount of analytes without the need for a labeled molecule.See, e.g., U.S. Pat. Nos. 5,631,171; and 5,955,377, each of which ishereby incorporated by reference in its entirety, including all tables,figures and claims. One skilled in the art also recognizes that roboticinstrumentation including but not limited to Beckman Access, AbbottAxSym, Roche ElecSys, Dade Behring Stratus systems are among theimmunoassay analyzers that are capable of performing the immunoassaystaught herein. Specific immunological binding of the antibody to themarker can be detected directly or indirectly. Direct labels includefluorescent or luminescent tags, metals, dyes, radionuclides, and thelike, attached to the antibody. Indirect labels include various enzymeswell known in the art, such as alkaline phosphatase, horseradishperoxidase and the like.

The use of immobilized antibodies specific for the one or morepolypeptides is also contemplated by the present invention. Theantibodies could be immobilized onto a variety of solid supports, suchas magnetic or chromatographic matrix particles, the surface of an assayplace (such as microtiter wells), pieces of a solid substrate materialor membrane (such as plastic, nylon, paper), and the like. An assaystrip could be prepared by coating the antibody or a plurality ofantibodies in an array on solid support. This strip could then be dippedinto the test sample and then processed quickly through washes anddetection steps to generate a measurable signal, such as ‘a coloredspot.

The analysis of a plurality of polypeptides may be carried outseparately or simultaneously with one test sample. For separate orsequential assay, suitable apparatuses include clinical laboratoryanalyzers such as the ElecSys (Roche), the AxSym (Abbott), the Access(Beckman), the ADVIA® CENTAUR® (Bayer) immunoassay systems, the NICHOLSADVANTAGE® (Nichols Institute) immunoassay system, etc. Preferredapparatuses or protein chips perform simultaneous assays of a pluralityof polypeptides on a single surface. Particularly useful physicalformats comprise surfaces having a plurality of discrete, addressablelocations for the detection of a plurality of different analytes. Suchformats include protein microarrays, or “protein chips” (see, e.g., Ngand Ilag, J. Cell Mol. Med. 6: 329-340 (2002)) and certain capillarydevices (see, e.g., U.S. Pat. No. 6,019,944). In these embodiments, eachdiscrete surface location may comprise antibodies to immobilize one ormore analyte(s) (e.g., one or more polypeptides of the invention) fordetection at each location. Surfaces may alternatively comprise one ormore discrete particles (e.g., microparticles or nanoparticles)immobilized at discrete locations of a surface, where the microparticlescomprise antibodies to immobilize one analyte (e.g., one or morepolypeptides of the invention) for detection.

In addition, one skilled in the art would recognize the value of testingmultiple samples (for example, at successive time points) from the sameindividual. Such testing of serial samples will allow the identificationof changes in polypeptide levels over time. Increases or decreases inpolypeptide levels, as well as the absence of change in such levels,would provide useful information about the disease status that includes,but is not limited to identifying the approximate time from onset of theevent, the presence and amount of salvageable tissue, theappropriateness of drug therapies, the effectiveness of varioustherapies as indicated by reperfusion or resolution of symptoms,differentiation of the various types of disease having similar symptoms,identification of the severity of the event, identification of thedisease severity, and identification of the patient's outcome, includingrisk of future events.

A panel consisting of the polypeptides referenced above, and optionallyincluding other protein markers useful in diagnosis, prognosis, ordifferentiation of disease, may be constructed to provide relevantinformation related to differential diagnosis. Such a panel may beconstructed to detect 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or more orindividual analytes, including one or more polypeptides of the presentinvention. The analysis of a single analyte or subsets of analytes couldbe carried out by one skilled in the art to optimize clinicalsensitivity or specificity in various clinical settings. These include,but are not limited to ambulatory, urgent care, critical care, intensivecare, monitoring unit, inpatient, outpatient, physician office, medicalclinic, and health screening settings. Furthermore, one skilled in theart can use a single analyte or a subset of analytes in combination withan adjustment of the diagnostic threshold in each of the aforementionedsettings to optimize clinical sensitivity and specificity. The clinicalsensitivity of an assay is defined as the percentage of those with thedisease that the assay correctly predicts, and the specificity of anassay is defined as the percentage of those without the disease that theassay correctly predicts (Tietz Textbook of Clinical Chemistry, 2^(nd)edition, Carl Burtis and Edward Ashwood eds., W.B. Saunders and Company,p. 496).

The analysis of analytes could be carried out in a variety of physicalformats as well. For example, the use of microtiter plates or automationcould be used to facilitate the processing of large numbers of testsamples. Alternatively, single sample formats could be developed tofacilitate immediate treatment and diagnosis in a timely fashion, forexample, in ambulatory transport or emergency room settings.

As discussed above, samples may continue to degrade the natriureticpeptides or fragments thereof, even once the sample is obtained. Thus,it may be advantageous to add one or more protease inhibitors to samplesprior to assay. Numerous protease inhibitors are known to those of skillin the art, and exemplary inhibitors may be found in, e.g., The CompleteGuide for Protease Inhibition, Roche Molecular Biochemicals, updatedJun. 3, 1999 athttp://www.roche-applied-science.com/fst/products.htm?/prod_inf/manuals/protease/prot_toc.htm,and European Patent Application 03013792.1 (published as EP 1 378 242A1), each of which is hereby incorporated in its entirety. Becausevarious metalloproteases and calcium-dependent proteases are known toexist in blood-derived samples, chelators such as EGTA and/or EDTA, alsoact as protease inhibitors. In addition, or in the alternative,inhibitors of neutral endopeptidase and/or DPPs may be used.

Inhibition of Natriuretic Peptide Degradation by Prolyl-Specific DPPs

The neurohumoral regulatory system of which natriuretic peptides are apart represents a complex system of cardiovascular regulation. Diseasessuch as congestive heart failure are, in essence, fatal diseases forwhich life may be prolonged, but the underlying disease never cured.Thus, there remains a need for novel therapeutic approaches to themanagement of the underlying diseases, and multiple points in thiscomplex system are seen as important targets by clinicians. The clinicalsuccess of angiotensin converting enzyme (“ACE”) inhibitors in diseasemanagement has led to a search for additional approaches that indirectlyaffect the course of cardiovascular disease by affecting enzymes thatact on vasoactive hormones.

In the case of the natriuretic hormones, increasing hormone levels havebeen found to have therapeutic potential in patients. See, e.g.,Tsekoura et al., Hellenic J. Cardiol. 44: 266-70, 2003. Neutralendopeptidase (“NEP”) is believed to be a key degradation mediator. Notsurprisingly, inhibitors of NEP have found use in treating patients withdiseases such as hypertension, atherosclerosis, and heart failure. See,e.g., Corti et al., Circulation 104: 1856-62, 2001. Combinationtreatment with both BNP and NEP inhibitors has been reported to producea synergistic effect on cardiac output reduced vascular resistance, andunloading of the heart. Chen et al., Circulation 105: 999-1003, 2002.Targeting NEP may suffer from the limitation, however, that NEPmetabolizes a broad range of biologically active peptides. See, e.g.,Walter et al., Curr. Opin. Nephrol. Hypertens. 6: 468-73, 1997.

The present invention describes a novel approach to treatment ofcardiovascular disease, particularly heart failure. Several natriureticpeptides, including human forms of pro-BNP, mature BNP, and pro-ANPcomprise a penultimate proline residue, rendering the peptides suitablesubstrates for prolyl-specific dipeptidyl dipeptidases (“DPPs”)Inhibitors of DPP have been described as having utility in themanagement of diabetes, mediated by the inhibition of glucose-dependentinsulinotropic polypeptide degradation by DPP IV. See, e.g., Gault etal., Biochem. Biophys. Res. Commun. 22: 207-13, 2003. However, their usein treatment of cardiovascular disease has not previously been reported.

Methods for preparing and identifying selective DPP inhibitors are wellknown in the art. DPP inhibitors include the dipeptide analoguesXaa-boroPro, including Pro-boroPro, Ala-boroPro, Val-boroPro, andLys-boroPro, and dab-pip. See, e.g., Senten et al., Bioorg. Med. Chem.Lett. 12: 2825-28, 2002; Jones et al., Blood, prepublished online May 8,2003; DOI 10.1182. Combinatorial chemistry methods have been used torapidly synthesize and screen numerous additional dipeptide analogueinhibitors of DPP. See, e.g., Leiting et al., Biochem. J. 371: 525-32,2003; Sedo et al., Physiol. Res. 52: 367-72, 2003; Villhauer et al., J.Med. Chem. 46: 2774-89, 2003; Senten et al., J. Comb, Chem. 5: 336-44,2003; and U.S. Pat. Nos. 5,602,102; 6,573,287, 6,548,481, 6,432,969, and6,355,614. The compounds described in these publications may be used aslead compounds in identifying additional DPP inhibitors for use in themethods described herein. A variety of techniques are available in theart for generating combinatorial libraries of small organic molecules.See generally Blondelle et al. Trends Anal. Chem. 14: 83, 1995; U.S.Pat. Nos. 5,359,115, 5,362,899, 5,288,514, and 5,721,099; Chen et al.JAGS 116: 2661, 1994; Kerr et al. JACS 115: 252, 1993; WO92/10092,WO93/09668, WO 94/08051, WO93/20242 and WO91/07087. A variety oflibraries on the order of about 16 to 1,000,000 or more diversomers canbe synthesized and screened for a particular activity or property usingthe methods described therein.

Preferably, the inhibitors finding use in the invention are smallmolecules, meaning having a molecular weight of less than about 1000Daltons. Such inhibitors are well known in the art. See, e.g.,WO04/07468 and WO04/50022, and U.S. Pat. Nos. 6,710,040; 6,699,871;6,432,969; 6,303,661; 6,166,063; 6,124,305; 6,110,949; and 6,107,317,each of which is hereby incorporated by reference in its entirety.Preferred small molecule inhibitors are orally effective. DPP-inhibitoryantibody or antibody fragments may also find use in the methodsdescribed herein. In this case, antibodies may be generated to DPP andscreened (e.g., using the phage display methods described herein) toidentify antibodies that inhibit DPP activity on one or more natriureticpeptides of interest.

Compounds may be screened for inhibitory activity using isolated DPPenzymes, cell extracts, or blood derived samples as a source of enzyme,and isolated natriuretic peptides as substrates. Selection of theconditions to inhibit loss of the penultimate proline residue from atarget natriuretic peptide may depend on the type of aqueous mediumunder consideration (for example, inhibition in a blood sample mayrequire conditions that differ from inhibition in the circulation of anorganism). Selecting such conditions are within the skill of theartisan. The ability of test compounds and their correspondingpharmaceutically acceptable acid addition salts to inhibit DPP may alsobe demonstrated by employing a modified version of the assay describedin Kubota et al., Clin. Exp. Immunol. 89: 192-7, 1992. Confirmation ofthe presence or absence of the penultimate proline residue may beperformed using an immunoassay selected to be sensitive to the loss ofthis N-terminal portion of the molecule, or through the use of massspectrometry.

Proceeding to the next step, candidate compounds that modulate DPPactivity in cultured cells can be tested in animal models that arerelevant to the disease condition of interest. In these methods, labelednatriuretic peptide may be injected into a test animal, and the Ty, forclearance of the natriuretic peptide from the circulation may bedetermined in the presence and absence of the inhibitor. Preferredanimal models of DPP-dependent natriuretic peptide degradation includerats, mice, sheep, dogs, cats, and pigs.

As discussed above, combination treatment with DPP inhibitors and NEPinhibitors and/or natriuretic peptide(s) is contemplated by theinvention. In addition or as an alternative, a natriuretic peptide maybe provided as an analogue that has been stabilized to DPP activity, asdescribed for glucose-dependent insulinotropic polypeptide in Gault etal., Metabolism 52: 679-87, 2003. In preferred embodiments, libraries ofnatriuretic peptide analogs having one or more substituted, deleted,added, or modified amino acids may be screened for improved stability toDPP degradation. Such analogs preferably retain 50% or more of thenatriuretic activity of the parent natriuretic peptide.

When administered, the pharmaceutical preparations of the invention areapplied in pharmaceutically-acceptable amounts and inpharmaceutically-acceptably compositions. Such preparations mayroutinely contain salt, buffering agents, preservatives, compatiblecarriers, and optionally other therapeutic agents. When used inmedicine, the salts should be pharmaceutically acceptable, butnon-pharmaceutically acceptable salts may conveniently be used toprepare pharmaceutically-acceptable salts thereof and are not excludedfrom the scope of the invention. Such pharmacologically andpharmaceutically-acceptable salts include, but are not limited to, thoseprepared from the following acids: hydrochloric, hydrobromic, sulfuric,nitric, phosphoric, maleic, acetic, salicylic, citric, formic, malonic,succinic, and the like. Also, pharmaceutically-acceptable salts can beprepared as alkaline metal or alkaline earth salts, such as sodium,potassium or calcium salts. The pharmaceutical compositions also maycontain, optionally, suitable preservatives, such as: benzalkoniumchloride; chlorobutanol; parabens and thimerosal. Carrier formulationsuitable for oral, subcutaneous, intravenous, intramuscular, etc.administrations can be found in Remington's Pharmaceutical Sciences,Mack Publishing Co., Easton, Pa.

A variety of administration routes are available for treating a subject.The particular mode of delivery selected will depend upon the particularcompound selected, the severity of the condition being treated and thedosage required for therapeutic efficacy. The methods of the invention,generally speaking, may be practiced using any mode of administrationthat is medically acceptable, meaning any mode that produces effectivelevels of the active compounds without causing clinically unacceptableadverse effects. Such modes of administration include oral, rectal,topical, nasal, interdermal, intravenous or parenteral routes. Suchmodes of administration also include obtaining T cells or bone marrowcells, stem cells or early lineage progenitor cells from a patient andcontacting the isolated cells with the compounds of the invention exvivo, followed by reintroducing the treated cells to the patient. Thetreated cells can be reintroduced to the patient in any manner known inthe art for administering viable cells.

Oral administration is particularly preferred. Compositions suitable fororal administration may be presented as discrete units, such ascapsules, tablets, lozenges, each containing a predetermined amount ofthe compound of the invention. Other compositions include suspensions inaqueous liquids or non-aqueous liquids such as a syrup, elixir or anemulsion. Preferably, the oral preparation does not include an entericcoating since it is desirable to expose the cyclic compounds of theinvention to the acidic pH conditions of the digestive tract to convertthe cyclic molecules to their linear counterparts.

Other delivery systems can include time-release, delayed release orsustained release delivery systems. Such systems can avoid repeatedadministrations of the compounds described above, increasing convenienceto the subject and the physician. Many types of release delivery systemsare available and known to those of ordinary skill in the art. Theyinclude polymer base systems such as poly(lactide-glycolide),copolyoxalates, polycaprolactones, polyesteramides, polyorthoesters,polyhydroxybutyric acid, and polyanhydrides. Microcapsules of theforegoing polymers containing drugs are described in, for example, U.S.Pat. No. 5,075,109. Delivery systems also include non-polymer systemsthat are: lipids including sterols such as cholesterol, cholesterolesters and fatty acids or neutral fats such as mono-di- andtri-glycerides; hydrogel release systems; sylastic systems; peptidebased systems; wax coatings; compressed tablets using conventionalbinders and excipients; partially fused implants; and the like. Specificexamples include, but are not limited to: (a) erosional systems in whichthe compound is contained in a form within a matrix such as thosedescribed in U.S. Pat. Nos. 4,452,775, 4,667,014, 4,748,034 and5,239,660 and (b) diffusional systems in which an active componentpermeates at a controlled rate from a polymer such as described in U.S.Pat. Nos. 3,832,253, and 3,854,480. In addition, pump-based hardwaredelivery systems can be used, some of which are adapted forimplantation.

Use of a long-term sustained release implant may be particularlysuitable for treatment of chronic conditions. Long-term release, as usedherein, means that the implant is constructed and arranged to deliverytherapeutic levels of the active ingredient for at least 10 days, andpreferably 60 days. Long-term sustained release implants are well-knownto those of ordinary skill in the art and include some of the releasesystems described above.

The selected compounds are administered in effective amounts. Aneffective amount is a dosage of the compound sufficient to provide amedically desirable result. The effective amount will vary with theparticular condition being treated, the age and physical condition ofthe subject being treated, the severity of the condition, the durationof the treatment, the nature of the concurrent therapy (if any), thespecific route of administration and like factors within the knowledgeand expertise of the health practitioner. Generally, doses of activecompounds will be from about 0.001 mg/kg per day to 1000 mg/kg per day.It is expected that doses range of 0.001 to 100 mg/kg will be suitable,preferably orally and in one or several administrations per day. Lowerdoses will result from other forms of administration, such asintravenous administration. In the event that a response in a subject isinsufficient at the initial doses applied, higher doses (or effectivelyhigher doses by a different, more localized delivery route) may beemployed to the extent that patient tolerance permits. Multiple dosesper day are contemplated to achieve appropriate systemic levels ofcompounds.

EXAMPLES

The following examples serve to illustrate the present invention. Theseexamples are in no way intended to limit the scope of the invention.

Example 1 Blood Sampling

Blood is preferably collected by venous puncture using a 20 gaugemulti-sample needle and evacuated tubes, although fingertip puncture,plantar surface puncture, earlobe puncture, etc., may suffice for smallvolumes. For whole blood collection, blood specimens are collected bytrained study personnel in EDTA-containing blood collection tubes. Forserum collection, blood specimens are collected by trained studypersonnel in thrombin-containing blood collection tubes. Blood isallowed to clot for 5-10 minutes, and serum is separated from insolublematerial by centrifugation. For plasma collection, blood specimens arecollected by trained study personnel in citrate-containing bloodcollection tubes and centrifuged for ≧12 minutes. Samples may be kept at4° C. until use, or frozen at −20° C. or colder for longer term storage.Whole blood is preferably not frozen.

Example 2 Recombinant Antibody Preparation

Immunization of Mice with Antigens and Purification of RNA from MouseSpleens

Mice are immunized by the following method based on experience of thetiming of spleen harvest for optimal recovery of mRNA coding forantibody. Two species of mice are used: Balb/c (Charles RiverLaboratories, Wilmington, Mass.) and A/J (Jackson Laboratories, BarHarbor, Me.). Each of ten mice are immunized intraperitoneally withantigen using 50 μg protein in Freund's complete adjuvant on day 0, andday 28. Tests bleeds of mice are obtained through puncture of theretro-orbital sinus. If, by testing the titers, they are deemed high byELISA using biotinylated antigen immobilized via streptavidin, the miceare boosted with 50 μg of protein on day 70, 71 and 72, with subsequentsacrifice and splenectomy on day 77. If titers of antibody are notdeemed satisfactory, mice are boosted with 50 μg antigen on day 56 and atest bleed taken on day 63. If satisfactory titers are obtained, theanimals are boosted with 50 μg of antigen on day 98, 99, and 100 and thespleens harvested on day 105. Typically, a test bleed dilution of 1:3200or more results in a half maximal ELISA response to be consideredsatisfactory.

The spleens are harvested in a laminar flow hood and transferred to apetri dish, trimming off and discarding fat and connective tissue.Working quickly, spleens are macerated with the plunger from a sterile 5cc syringe in the presence of 1.0 ml of solution D (25.0 g guanidinethiocyanate (Boehringer Mannheim, Indianapolis, Ind.), 29.3 ml sterilewater, 1.76 ml 0.75 M sodium citrate (pH 7.0), 2.64 ml 10% sarkosyl(Fisher Scientific, Pittsburgh, Pa.), 0.36 ml 2-mercaptoethanol (FisherScientific, Pittsburgh, Pa.)). The spleen suspension is pulled throughan 18 gauge needle until viscous and all cells are lysed, thentransferred to a microcentrifuge tube. The petri dish is washed with 100μl of solution D to recover any remaining spleen, and this istransferred to the tube. The suspension is then pulled through a 22gauge needle an additional 5-10 times. The sample is divided evenlybetween two microcentrifuge tubes and the following added in order, withmixing by inversion after each addition: 100 μl 2 M sodium acetate (pH4.0), 1.0 ml water-saturated phenol (Fisher Scientific, Pittsburgh,Pa.), 200 μl chloroform/isoamyl alcohol 49:1 (Fisher Scientific,Pittsburgh, Pa.). The solution is vortexed for 10 seconds and incubatedon ice for 15 min. Following centrifugation at 14,000 rpm for 20 min at2-8° C., the aqueous phase is transferred to a fresh tube. An equalvolume of water saturated phenol/chloroform/isoamyl alcohol (50:49:1) isadded, and the tube vortexed for ten seconds. After a 15 min incubationon ice, the sample is centrifuged for 20 min at 2-8° C., and the aqueousphase transferred to a fresh tube and precipitated with an equal volumeof isopropanol at −20° C. for a minimum of 30 min. Followingcentrifugation at 14,000 rpm for 20 min at 4° C., the supernatant isaspirated away, the tubes briefly spun and all traces of liquid removed.The RNA pellets are each dissolved in 300 μl of solution D, combined,and precipitated with an equal volume of isopropanol at −20° C. for aminimum of 30 min. The sample is centrifuged 14,000 rpm for 20 min at 4°C., the supernatant aspirated as before, and the sample rinsed with 100μl of ice-cold 70% ethanol. The sample is again centrifuged 14,000 rpmfor 20 min at 4° C., the 70% ethanol solution aspirated, and the RNApellet dried in vacuo. The pellet is resuspended in 100 μl of steriledistilled water. The concentration is determined by A260 using anabsorbance of 1.0 for a concentration of 40 μg/ml. The RNA is stored at−80° C.

Preparation of Complementary DNA (cDNA)

The total RNA purified as described above is used directly as templatefor preparation of cDNA. RNA (50 μg) is diluted to 100 μL with sterilewater, and 10 μL-130 ng/mL oligo dT₁₂ is added. The sample is heated for10 min at 70° C., then cooled on ice. 40 μL 5× first strand buffer isadded (Gibco/BRL, Gaithersburg, Md.), 20 μL 0.1 M dithiothreitol(Gibco/BRL, Gaithersburg, Md.), 10 μL 20 mM deoxynucleosidetriphosphates (dNTP's, Boehringer Mannheim, Indianapolis, Ind.), and 10μL water on ice. The sample is then incubated at 37° C. for 2 min. 10 μLreverse transcriptase (Superscript™ II, Gibco/BRL, Gaithersburg, Md.) isadded and incubation continued at 37° C. for 1 hr. The cDNA products areused directly for polymerase chain reaction (PCR).

Amplification of cDNA by PCR

To amplify substantially all of the H and L chain genes using PCR,primers are chosen that corresponded to substantially all publishedsequences. Because the nucleotide sequences of the amino terminals of Hand L contain considerable diversity, 33 oligonucleotides aresynthesized to serve as 5′ primers for the H chains, and 29oligonucleotides are synthesized to serve as 5′ primers for the kappa Lchains, as described in U.S. 20030104477. The 5′ primers are madeaccording to the following criteria. First, the second and fourth aminoacids of the L chain and the second amino acid of the heavy chain areconserved. Mismatches that change the amino acid sequence of theantibody are allowed in any other position. Second, a 20 nucleotidesequence complementary to the M13 uracil template is synthesized on the5′ side of each primer. This sequence is different between the H and Lchain primers, corresponding to 20 nucleotides on the 3′ side of thepelB signal sequence for L chain primers and the alkaline phosphatasesignal sequence for H chain primers. The constant region nucleotidesequences require only one 3′ primer each to the H chains and the kappaL chains (FIG. 2). Amplification by PCR was performed separately foreach pair of 5′ and 3′ primers. A 50 μL reaction is performed for eachprimer pair with 50 pmol of 5′ primer, 50 pmol of 3′ primer, 0.25 μL TaqDNA Polymerase (5 units/μL, Boehringer Mannheim, Indianapolis, Ind.), 3μL cDNA (described in Example 2), 5 μL 2 mM dNTP's, 5 μL 10× Taq DNApolymerase buffer with MgCl₂ (Boehringer Mannheim, Indianapolis, hid.),and H₂O to 50 μL Amplification is done using a GeneAmp® 9600 thermalcycler (Perkin Elmer, Foster City, Calif.) with the following program:94° C. for 1 mM; 30 cycles of 94° C. for 20 sec, 55° C. for 30 sec, and72° C. for 30 sec; 72° C. for 6 min; 4° C.

The dsDNA products of the PCR process are then subjected to asymmetricPCR using only 3′ primer to generate substantially only the anti-sensestrand of the target genes. A 100 μL reaction is done for each dsDNAproduct with 200 pmol of 3′ primer, 2 μL of ds-DNA product, 0.5 μL TaqDNA Polymerase, 10 μL 2 mM dNTP's, 10 μL 10× Taq DNA polymerase bufferwith MgCl₂ (Boehringer Mannheim, Indianapolis, Ind.), and H₂O to 100 μL.The same PCR program as that described above is used to amplify thesingle-stranded (ss)-DNA.

Purification of SS-DNA by High Performance Liquid Chromatography andKinasing Ss-DNA

The H chain ss-PCR products and the L chain ss-PCR products are ethanolprecipitated by adding 2.5 volumes ethanol and 0.2 volumes 7.5 Mammonium acetate and incubating at −20° C. for at least 30 min. The DNAis pelleted by centrifuging in an Eppendorf centrifuge at 14,000 rpm for10 mM at 2-8° C. The supernatant is carefully aspirated, and the tubesbriefly spun a 2nd time. The last drop of supernatant is removed with apipet. The DNA is dried in vacuo for 10 min on medium heat. The H chainproducts are pooled in 210 μL water and the L chain products are pooledseparately in 210 μL water. The ss-DNA is purified by high performanceliquid chromatography (HPLC) using a Hewlett Packard 1090 HPLC and aGen-Pak™ FAX anion exchange column (Millipore Corp., Milford, Mass.) atan oven temperature of 60° C. Absorbance is monitored at 260 nm. Thess-DNA eluted from the HPLC is collected in 0.5 min fractions. Fractionscontaining ss-DNA are ethanol precipitated, pelleted and dried asdescribed above. The dried DNA pellets are pooled in 200 μL sterilewater.

If desired, the ss-DNA is kinased on the 5′ end in preparation formutagenesis. 24 μL 10× kinase buffer (United States Biochemical,Cleveland, Ohio), 10.4 μL 10 mM adenosine-5′-triphosphate (BoehringerMannheim, Indianapolis, Ind.), and 24, polynucleotide kinase (30units/μL, United States Biochemical, Cleveland, Ohio) is added to eachsample, and the tubes are incubated at 37° C. for 1 hr. The reactionsare stopped by incubating the tubes at 70° C. for 10 min. The DNA ispurified with one extraction of equilibrated phenol (pH>8.0, UnitedStates Biochemical, Cleveland, Ohio)-chloroform-isoamy-1 alcohol(50:49:1) and one extraction with chloroform: isoamyl alcohol (49:1).After the extractions, the DNA is ethanol precipitated and pelleted asdescribed above. The DNA pellets are dried, then dissolved in 50 μLsterile water. The concentration is determined by measuring theabsorbance of an aliquot of the DNA at 260 nm using 33 μg/mL for anabsorbance of 1.0. Samples are stored at −20° C.

Antibody Phage Display Vector

The antibody phage display vector for cloning antibodies is derived froman M13 vector supplied by Ixsys, designated 668-4. The vector 668-4contained the DNA sequences encoding the heavy and light chains of amouse monoclonal Fab fragment inserted into a vector described by Huse,WO 92/06024. The vector has a Lac promoter, a pelB signal sequence fusedto the 5′ side of the L chain variable region of the mouse antibody, theentire kappa chain of the mouse antibody, an alkaline phosphatase signalsequence at the 5′ end of the H chain variable region of the mouseantibody, the entire variable region and the first constant region ofthe H chain, and 5 codons of the hinge region of an IgG1 H chain. Adecapeptide sequence is at the 3′ end of the H chain hinge region and anamber stop codon separates the decapeptide sequence from the pseudo-geneVIII sequence. The amber stop allows expression of H chain fusionproteins with the gene VIII protein in. E. coli suppressor strains suchas XL1 blue (Stratagene, San Diego, Calif.), but not in nonsuppressorcell strains such as MK30 (Boehringer Mannheim, Indianapolis, Ind.) (seeFIG. 3A).

To make the first derivative cloning vector, deletions are made in thevariable regions of the H chain and the L chain by oligonucleotidedirected mutagenesis of a uracil template (Kunkel, Proc. Natl. Acad.Sci. USA 82:488 (1985); Kunkel, et al., Methods. Enzymol. 154:367(1987)). These mutations delete the region of each chain from the 5′ endof CDR1 to the 3′ end of CDR3, and the mutations add a DNA sequencewhere protein translation would stop (see FIG. 4 for mutagenesisoligonucleotides). This prevents the expression of H or L chain constantregions in clones without an insert, thereby allowing plaques to bescreened for the presence of insert. The resulting cloning vector iscalled BS11.

Many changes are made to BS11 to generate the cloning vector used in thepresent screening methods. The amber stop codon between the heavy chainand the pseudo gene VIII sequence is removed so that every heavy chainis expressed as a fusion protein with the gene VIII protein. Thisincreases the copy number of the antibodies on the phage relative toBS11. A HindIII restriction enzyme site in the sequence between the 3′end of the L chain and the 5′ end of the alkaline phosphatase signalsequence is deleted so antibodies can be subcloned into a pBR322derivative. The interchain cysteine residues at the carboxyl-terminus ofthe L and H chains are changed to serine residues. This increases thelevel of expression of the antibodies and the copy number of theantibodies on the phage without affecting antibody stability.Nonessential DNA sequences on the 5′ side of the lac promoter and on the3′ side of the pseudo gene VIII sequence are deleted to reduce the sizeof the M13 vector and the potential for rearrangement. A transcriptionalstop DNA sequence is added to the vector at the L chain cloning site inaddition to the translational stop so that phage with only heavy chainproteins on their surface, which might bind nonspecifically in panning,are not made. Finally, DNA sequences for protein tags are added todifferent vectors to allow enrichment for polyvalent phage by metalchelate chromatography (polyhistidine sequence) or by affinitypurification using a decapeptide tag and a magnetic latex having animmobilized antibody that binds the decapeptide tag. The vector BS39 hasa polyhistidine sequence at the 3′ end of the kappa chain with no tag atthe end of the heavy chain, while BS45 has a polyhistidine sequencebetween the end of the heavy chain constant region and the pseudo-geneVIII sequence, and a decapeptide sequence at the 3′ end of the kappachain constant region.

Preparation of Uracil Templates Used in Generation of Spleen AntibodyPhage Libraries

1 mL of E. coli CJ236 (BioRAD, Hercules, Calif.) overnight culture isadded to 50 ml 2×YT in a 250 mL baffled shake flask. The culture isgrown at 37° C. to OD₆₀₀=0.6, inoculated with 10 μl of a 1/100 dilutionof vector phage stock and growth continued for 6 hr. Approximately 40 mLof the culture is centrifuged at 12,000 rpm for 15 minutes at 4° C. Thesupernatant (30 mL) is transferred to a fresh centrifuge tube andincubated at room temperature for 15 minutes after the addition of 15 μlof 10 mg/ml RNAseA (Boehringer Mannheim, Indianapolis, Ind.). The phageare precipitated by the addition of 7.5 ml of 20% polyethylene glycol8000 (Fisher Scientific, Pittsburgh, Pa.)/3.5M ammonium acetate (SigmaChemical Co., St. Louis, Mo.) and incubated on ice for 30 min. Thesample is centrifuged at 12,000 rpm for 15 min at 2-8° C. Thesupernatant is carefully discarded, and the tube is briefly spun toremove all traces of supernatant. The pellet is resuspended in 400 μl ofhigh salt buffer (300 mM NaCl, 100 mM Tris pH 8.0, 1 mM EDTA), andtransferred to a 1.5 mL tube. The phage stock is extracted repeatedlywith an equal volume of equilibrated phenol:chloroform:isoamyl alcohol(50:49:1) until no trace of a white interface is visible, and thenextracted with an equal volume of chloroform:isoamyl alcohol (49:1). TheDNA is precipitated with 2.5 volumes of ethanol and ⅕ volume 7.5 Mammonium acetate and incubated 30 min at −20° C. The DNA is centrifugedat 14,000 rpm for 10 mM at 4° C., the pellet washed once with cold 70%ethanol, and dried in vacuo. The uracil template DNA is dissolved in 30μl sterile water and the concentration determined by A260 using anabsorbance of 1.0 for a concentration of 40 μg/ml. The template isdiluted to 250 ng/μl with sterile water, aliquoted, and stored at −20°C.

Mutagenesis of Uracil Template with Ss-DNA and Electroporation into E.coli to Generate Antibody Phage Libraries

Antibody phage-display libraries are generated by simultaneouslyintroducing single-stranded heavy and light chain genes onto aphage-display vector uracil template. A typical mutagenesis is performedon a 2 μg scale by mixing the following in a 0.2 mL PCR reaction tube: 8μl of (250 ng/μl) uracil template (examples 5 and 6), 8 μl of 10×annealing buffer (200 mM Tris pH 7.0, 20 mM MgCl₂, 500 mM NaCl), 3.33 μlof kinased single-stranded heavy chain insert (100 ng/μl), 3.1 μl ofkinased single-stranded light chain insert (100 ng/ml), and sterilewater to 80 μl. DNA is annealed in a GeneAmp® 9600 thermal cycler usingthe following thermal profile: 20 sec at 94° C., 85° C. for 60 sec, 85°C. to 55° C. ramp over 30 min, hold at 55° C. for 15 min. The DNA istransferred to ice after the program finishes. The extension/ligation iscarried out by adding 8 μl of 10× synthesis buffer (5 mM each dNTP, 10mM ATP, 100 mM Tris pH 7.4, 50 mM MgCl₂, 20 mM DTT), 8 μl T4 DNA ligase(1 U/μl, Boehringer Mannheim, Indianapolis, Ind.), 8 μl diluted T7 DNApolymerase (1 U/μl, New England BioLabs, Beverly, Mass.) and incubatedat 37° C. for 30 mM. The reaction is stopped with 300 μl of mutagenesisstop buffer (10 mM Tris pH 8.0, 10 mM EDTA). The mutagenesis DNA isextracted once with equilibrated phenol (pH>8):chloroform:isoamylalcohol (50:49:1), once with chloroform:isoamyl alcohol (49:1), and theDNA is ethanol precipitated at −20° C. for at least 30 min. The DNA ispelleted and the supernatant carefully removed as described above. Thesample is briefly spun again and all traces of ethanol removed with apipetman. The pellet is dried in vacuo. The DNA is resuspended in 4 μlof sterile water.

1 μl mutagenesis DNA is (500 ng) is transferred into 40 μlelectrocompetent E. coli DH12S (Gibco/BRL, Gaithersburg, Md.). Thetransformed cells are mixed with 1.0 mL 2×YT broth and transferred to 15mL sterile culture tubes. The first round antibody phage is made byshaking the cultures overnight at 23° C. and 300 rpm. The efficiency ofthe electroporation is measured by plating 10 μl of 10⁻³ and 10⁻⁴dilutions of the cultures on LB agar plates. These plates are incubatedovernight at 37° C. The efficiency is determined by multiplying thenumber of plaques on the 10⁻³ dilution plate by 10⁵ or multiplying thenumber of plaques on the 10⁴ dilution plate by 10⁶. The overnightcultures from the electroporations are transferred to 1.5 ml tubes, andthe cells are pelleted by centrifuging at 14,000 rpm for 5 min. Thesupernatant, which is the first round of antibody phage, is thentransferred to 15 mL sterile centrifuge tubes with plug seal caps.

Transformation of E. coli by Electroporation

The electrocompetent E. coli cells are thawed on ice. DNA is mixed with20-40 μL electrocompetent cells by gently pipetting the cells up anddown 2-3 times, being careful not to introduce air-bubbles. The cellsare transferred to a Gene Pulser cuvette (0.2 cm gap, BioRAD, Hercules,Calif.) that has been cooled on ice, again being careful not tointroduce an air-bubble in the transfer. The cuvette is placed in the E.coli Pulser (BioRAD, Hercules, Calif.) and electroporated with thevoltage set at 1.88 kV according to the manufacturer's recommendation.The transformed sample is immediately diluted to 1 ml with 2× YT brothand processed as procedures dictate.

Preparation of Biotinylated Antigens and Antibodies

Protein antigens or antibodies are dialyzed against a minimum of 100volumes of 20 mM borate, 150 mM NaCl, pH 8 (BBS) at 2-8° C. for at least4 hr. The buffer is changed at least once prior to biotinylation.Protein antigens or antibodies are reacted with biotin-XX-NHS ester(Molecular Probes, Eugene, Oreg., stock solution at 40 mM indimethylformamide) at a final concentration of 1 mM for 1 hr at roomtemperature. After 1 hr, the protein antigens or antibodies areextensively dialyzed into BBS to remove unreacted small molecules.

Preparation of Alkaline Phosphatase-Antigen Conjugates

Alkaline phosphatase (AP, Calzyme Laboratories, San Luis Obispo, Calif.)is placed into dialysis versus a minimum of 100 volumes of column buffer(50 mM potassium phosphate, 10 mM borate, 150 mM NaCl, 1 mM MgSO₄, pH7.0) at 2-8° C. for at least four hr. The buffer is changed at leasttwice prior to use of the AP. When the AP is removed from dialysis andbrought to room temperature, the concentration is determined byabsorbance at 280 nm using an absorbance of 0.77 for a 1 mg/mL solution.The AP is diluted to 5 mg/mL with column buffer. The reaction of AP andsuccinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC,Pierce Chemical Co., Rockford, Ill.) is carried out using a 20:1 ratioof SMCC:AP. SMCC is dissolved in acetonitrile at 20 mg/mL and diluted bya factor of 84 when added to AP while vortexing or rapidly stirring. Thesolution is allowed to stand at room temperature for 90 min before theunreacted SMCC and low molecular weight reaction products are separatedfrom the AP using gel filtration chromatography (G50 Fine, PharmaciaBiotech, Piscataway, N.J.) in a column equilibrated with column buffer.

Protein antigen is dialyzed versus a minimum of 100 volumes of 20 mMpotassium phosphate, 4 mM borate, 150 mM NaCl, pH 7.0 at 2-8° C. for atleast four hr. The buffer is changed at least twice prior to use of theantigen. The amount of antigen is quantitated by absorbance at 280 nm orby the method of Lowry. The reaction of antigen and N-succinimidyl3-[2-pyridyldithio]propionate (SPDP, Pierce Chemical Co., Rockford,Ill.) is carried out using a 20:1 molar ratio of SPDP:antigen. SPDP isdissolved in dimethylformamide at 40 mM and diluted into the antigensolution while vortexing. The solution is allowed to stand at roomtemperature for 90 min, at which time the reaction is quenched by addingtaurine (Aldrich Chemical Co., Milwaukee, Wis.) to a final concentrationof 20 mM for 5 min. Dithiothreitol (Fisher Scientific, Pittsburgh, Pa.)is added to the protein at a final concentration of 1 mM for 30 min. Thelow molecular weight reaction products are separated from the antigenusing gel filtration chromatography in a column equilibrated in 50 mMpotassium phosphate, 10 mM borate, 150 mM NaCl, 0.1 mM ethylene diaminetetraacetic acid (EDTA, Fisher Scientific, Pittsburgh, Pa.), pH 7.0.

The AP and antigen are mixed together in an equimolar ratio. Thereaction is allowed to proceed at room temperature for 2 hr. Theconjugate is diluted to 0.1 mg/mL with block containing 1% bovine serumalbumin (from 30% BSA, Bayer, Kankakee, Ill.), 10 mM Tris, 150 mM NaCl,1 mM MgCl₂, 0.1 mM ZnCl₂, 0.1% polyvinyl alcohol (80% hydrolyzed,Aldrich Chemical Co., Milwaukee, Wis.), pH 8.0.

Preparation of Avidin Magnetic Latex

Magnetic latex (Estapor, 10% solids, Bangs Laboratories, Fishers, Ind.)is thoroughly resuspended and 2 ml aliquoted into a 15 ml conical tube.The magnetic latex is suspended in 12 ml distilled water and separatedfrom the solution for 10 mM using a magnet. While still in the magnet,the liquid is carefully removed with a 10 mL sterile pipet. This washingprocess is repeated an additional three times. After the final wash, thelatex is resuspended in 2 ml of distilled water. In a separate 50 mlconical tube, 10 mg of avidin-HS (NeutrAvidin, Pierce, Rockford, Ill.)is dissolved in 18 ml of 40 mM Tris, 0.15 M sodium chloride, pH 7.5(TBS). While vortexing, the 2 ml of washed magnetic latex is added tothe diluted avidin-HS and the mixture vortexed an additional 30 seconds.This mixture is incubated at 45° C. for 2 hr, shaking every 30 minutes.The avidin magnetic latex is separated from the solution using a magnetand washed three times with 20 ml BBS as described above. After thefinal wash, the latex is resuspended in 10 ml BBS and stored at 4° C.

Immediately prior to use, the avidin magnetic latex is equilibrated inpanning buffer (40 mM TRIS, 150 mM NaCl, 20 mg/mL BSA, 0.1% Tween 20(Fisher Scientific, Pittsburgh, Pa.), pH 7.5). The avidin magnetic latexneeded for a panning experiment (200 μl/sample) is added to a sterile 15ml centrifuge tube and brought to 10 ml with panning buffer. The tube isplaced on the magnet for 10 min to separate the latex. The solution iscarefully removed with a 10 mL sterile pipet as described above. Themagnetic latex is resuspended in 10 mL of panning buffer to begin thesecond wash. The magnetic latex is washed a total of 3 times withpanning buffer. After the final wash, the latex is resuspended inpanning buffer to the initial aliquot volume.

Plating M13 Phage or Cells Transformed with Antibody Phage-DisplayVector Mutagenesis Reaction

The phage samples are added to 200 μL of an overnight culture of E. coliXL 1-Blue when plating on 100 mm LB agar plates or to 600 μL ofovernight cells when plating on 150 mm plates in sterile 15 ml culturetubes. After adding LB top agar (3 mL for 100 mm plates or 9 mL for 150mm plates, top agar stored at 55° C., Appendix A1, Molecular Cloning, ALaboratory Manual, (1989) Sambrook. J), the mixture is evenlydistributed on an LB agar plate that had been pre-warmed (37° C.-55° C.)to remove any excess moisture on the agar surface. The plates are cooledat room temperature until the top agar solidified. The plates areinverted and incubated at 37° C. as indicated.

Develop Nitrocellulose Filters with Alkaline Phosphatase Conjugates

After overnight incubation of the nitrocellulose filters on LB agarplates, the filters are carefully removed from the plates with membraneforceps and incubated for 2 hr in either casein block (block with 1%casein (Hammersten grade, Research Organics, Cleveland, Ohio)), whenusing antigen-AP conjugates or block when using goat anti-mouse kappa-AP(Southern Biotechnology Associates, Inc., Birmingham, Ala.). After 2 hr,the filters are incubated with the AP conjugate for 2-4 hr. Antigen-APconjugates are diluted into casein block at a final concentration of 1μg/mL and goat anti-mouse kappa-AP conjugates are diluted into block ata final concentration of 1 μg/mL. Filters are washed 3 times with 40 mMTRIS, 150 mM NaCl, 0.05% Tween 20, pH 7.5 (TBST) (Fisher Chemical,Pittsburgh, Pa.) for 5 mM each. After the final wash, the filters aredeveloped in a solution containing 0.2 M 2-amino-2-methyl-1-propanol(JBL Scientific, San Luis Obispo, Calif.), 0.5 M TRIS, 0.33 mg/mL nitroblue tetrazolium (Fisher Scientific, Pittsburgh, Pa.) and 0.166 mg/mL5-bromo-4-chloro-3-indolyl-phosphate, p-toluidine salt.

Enrichment of Polyclonal Phage to BNP Peptides with No Tags on the HeavyChain and a Polyhistidine Sequence on the Kappa Chain

This example describes multiple rounds of screening of a phage libraryto BNP peptides. Some of the rounds of screening are alternated withrounds of enrichment for phage displaying multiple copies of antibodies.The percentage of phage displaying any light chain, and the percentageof phage displaying Fab fragments with specific affinity for BNPpeptides of interest (referred to below as “antigen”) is measured aftereach round of screening.

The first round antibody phage is prepared as described above using BS39uracil template. Two electroporations of mutagenesis DNA hadefficiencies of 9.7×10⁷ PFU and 8.3×10⁷ PFU. The phage from bothelectroporations are combined and diluted to 3.2 ml with panning buffer.The phage is aliquoted into 2-1 mL aliquots in 15 mL disposable sterilecentrifuge tubes with plug seal caps. Antigen-biotin (10 μL, 10⁻⁶ Mstock concentration) is added to each phage aliquot. The phage samplesare incubated overnight at 2-8° C.

After the incubation, the phage samples are panned with avidin magneticlatex. The equilibrated avidin magnetic latex (see Example 11), 200 μLlatex per sample, is incubated with the phage for 10 min at roomtemperature. After 10 min, approximately 9 mL of panning buffer is addedto each phage sample, and the magnetic latex is separated from thesolution using a magnet. After 10 min in the magnet, the unbound phageis carefully removed with a 10 mL sterile pipet. The magnetic latex isthen resuspended in 10 mL of panning buffer to begin the second wash.The latex is washed a total of 5 times as described above. For eachwash, the tubes are in the magnet for 10 min to separate unbound phagefrom the magnetic latex. After the 5th wash, the magnetic latex isresuspended in 1 mL TBS and transferred to a 1.5 mL tube. Aliquots ofthe latex are taken at this point to plate on 100 mm LB agar plates asdescribed above. The bulk of the magnetic latex (99%) is resuspended in200 μL 2×YT and is plated on a 150 mm LB agar plate as described inExample 12. The 100 mm LB agar plates are incubated at 37° C. for 6-7hr, then the plates are transferred to room temperature andnitrocellulose filters (pore size 0.45 μm, BA85 Protran, Schleicher andSchuell, Keene, N.H.) are overlayed onto the plaques. Plates withnitrocellulose filters are incubated overnight at room temperature. The150 mm plates are used to amplify the phage binding to the magneticlatex to generate the next round of antibody phage. These plates areincubated at 37° C. for 4 hr, then overnight at 20° C.

After the overnight incubation, the antibody phage is eluted from the150 mm plates, and the filters are developed with alkalinephosphatase-antigen as described herein. The antibody phage is elutedfrom the 150 mm plates by pipetting 8 mL 2YT media onto the lawn andgently shaking the plate at room temperature for 20 min. The phage aretransferred to a 15 mL disposable sterile centrifuge tubes with plugseal cap and the debris from the LB plate is pelleted by centrifugingfor 15 min at 3500 rpm. The 2nd round antibody phage is then transferredto a new tube.

To begin the 2nd round of panning, the antibody phage are titered byplating 10 μL of 10⁻⁷ and 10⁻⁸ dilutions of the phage on 100 mm LB agarplates. The plates are incubated at 37° C. for 6-7 hr, then the numberof plaques on the plates are counted. Also, to monitor the percentage ofkappa positives in the antibody phage, a nitrocellulose filter isoverlayed onto the plate and incubated overnight at room temperature.The percentage of kappa positives is a measure of the proportion ofphage displaying intact Fab fragments.

Both 2nd round antibody phage samples are pooled by diluting each sampleinto panning buffer at a final concentration of 5×10⁹ PFU/mL to a finalvolume of 1 mL. (The titers of the antibody phage are about 2×10¹²PFU/mL and 1.7×10¹²). Antigen-biotin (10 μL, 10⁻⁶ M stock concentration)is added to the phage and the phage is incubated at 2-8° C. overnight.The nitrocellulose filters on the antibody phage titer plates aredeveloped with goat anti-mouse kappa AP as described herein. The secondround antibody phage is panned with avidin magnetic latex as describedabove. After washing the latex with panning buffer, the latex isresuspended in 1 mL TBS and transferred to a 1.5 mL tube. Aliquots ofthe latex are plated on 100 mm LB agar plates as described above tocheck functional positives, and the rest of the latex is plated on 150mm LB agar plates to generate the 3rd round antibody phage. This generalprocedure of titering the antibody phage, diluting the phage intopanning buffer and adding antigen-biotin, incubating the phage at least16 hr at 2-8° C., panning the phage with avidin magnetic latex, andplating the magnetic latex is followed through 10 rounds of panning. Theonly changes from that described above is the concentration ofantigen-biotin is lower to increase the affinity of bound antibodies,and the number of phage panned is between 10¹⁰ and 10⁸.

After the 10th round of panning to antigen-biotin, the antibody phageare subject to a round of enrichment for polyvalent display. Enrichmentis effected by binding of the hexahistidine tag fused to the displayedlight chain to Ni NTA agarose (Qiagen Inc., Chatsworth, Calif.). The11th round antibody phage (2.5 mL) are diluted into 2.5 mL panningbuffer in a 15 mL disposable sterile centrifuge tube with plug seal cap.The Ni NTA is equilibrated into panning buffer using the followingprocedure. The resin (1 mL per phage sample) is diluted to 50 mL withpanning buffer in a 50 mL disposable sterile centrifuge tube with plugseal cap and then is pelleted in an IEC centrifuge at 500 rpm for 1 min.The supernatant is carefully removed with a 50 mL disposable pipet, andthe resin is again diluted to 50 mL with panning buffer for the secondwash. The resin is washed in this manner a total of 4 times in order toequilibrate the resin in panning buffer. The equilibrated resin is thenresuspended to its original volume with panning buffer. Equilibratedresin (1 mL) is then added to the phage, and the tube is gently rockedfor 15 min. After 15 min, the resin is pelleted in an IEC centrifuge at500 rpm for 1 min. The supernatant is gently removed with a 10 mLdisposable pipet, and the resin is resuspended in 10 mL panning bufferfor the first wash. The resin is pelleted as described above, thesupernatant is removed, and the resin is resuspended a 2nd time in 10 mLpanning buffer. This procedure is repeated for a total of 5 panningbuffer washes. After the 5th wash is removed, the resin is resuspendedin 1 mL of elution buffer (50 mM citrate, 150 mM NaCl, pH 4.0) andtransferred to a 1.5 mL tube. The resin is gently rocked for 1 hr toelute the antibody phage. After 1 hr, the resin is pelleted (14,000 rpmin Eppendorf centrifuge for 5 min), and the phage is removed while beingcareful not to transfer any resin. In order to adjust the pH of thephage solution to 8, 50 μL of 1 M Tris, pH 8.3 and 46 μL of 1 M NaOH areadded to the 1 mL phage sample. Also, 10 1 L of 300 mg/mL bovine serumalbumin (Bayer, Kankakee, Ill.) is added to the phage sample. Theresulting phage solution (1 mL) is transferred to a 15 mL disposablesterile centrifuge tube with plug seal cap for the 11th round of panningwith antigen-biotin, as described above.

The 12th-14th rounds of panning are done as described above, where theantibody phage is bound to Ni NTA, eluted, and the eluted phage pannedwith antigen-biotin. However, in round 13, unlabeled C-terminal BNPpeptides are added to the phage eluted from the Ni NTA at 100-fold molarexcess to the antigen-biotin to select antibodies that specifically bindto antigen without binding to the C-terminal BNP peptides.

Example 3 Biochemical Analyses

BNP is measured using standard immunoassay techniques. These techniquesinvolve the use of antibodies to specifically bind the protein targets.An antibody directed against BNP is biotinylated usingN-hydroxysuccinimide biotin (NHS-biotin) at a ratio of about 5NHS-biotin moieties per antibody. The biotinylated antibody is thenadded to wells of a standard avidin 384 well microtiter plate, andbiotinylated antibody not bound to the plate is removed. This formed ananti-BNP solid phase in the microtiter plate. Another anti-BNP antibodyis conjugated to alkaline phosphatase using standard techniques, usingSMCC and SPDP (Pierce, Rockford, Ill.). The immunoassays are performedon a TECAN Genesis RSP 200/8 Workstation. Test samples (10 μL) arepipetted into the microtiter plate wells, and incubated for 60 min. Thesample is then removed and the wells washed with a wash buffer,consisting of 20 mM borate (pH 7.42) containing 150 mM NaCl, 0.1% sodiumazide, and 0.02% Tween-20. The alkaline phosphatase-antibody conjugateis then added to the wells and incubated for an additional 60 min, afterwhich time, the antibody conjugate is removed and the wells washed witha wash buffer. A substrate, (AttoPhos®, Promega, Madison, Wis.) is addedto the wells, and the rate of formation of the fluorescent product isrelated to the concentration of the BNP in the test samples.

Example 4 Synthesis of DPP Inhibitors

Peptide coupling chemistry is preferably employed to prepare linearboroPro compounds. The peptide coupling chemistry methods and proceduresused in this invention are readily available. Examples of books usingthese methods include, but are not limited to, the following citationsincorporated herein by reference: P. D. Bailey, “An Introduction toPeptide Chemistry,” John Wiley & Sons, 1990; Miklos Bodansky, “PeptideChemistry A Practical Textbook,” Springer-Verlag, 1988; Miklos Bodansky,“Principles of Peptide Synthesis, Reactivity and Structure Concepts inOrganic Chemistry,” Volume 16, Springer-Verlag, 1984; and MiklosBodansky, “Principles of Peptide Synthesis, Reactivity and StructureConcepts in Organic Chemistry,” Volume 21, Springer-Verlag, 1984.

The compounds of the invention can begin with the synthesis of H-boroProas disclosed in WO 98/00439. Use of H-boroPro is for illustrativepurposes only, and is not intended to limit the scope of this invention.According to WO 98/00439, H-boroPro may be prepared by the syntheticroute previously developed and described (G. R. Flentke, et al.,“Inhibition of dipeptidyl aminopeptidase IV (DP-IV) by Xaa-boroProdipeptides and use of these inhibitors to examine the role of DP-IV inT-cell function,” PNAS (U.S.A.) 88, 1556-1559 (1991); also described inU.S. Pat. No. 5,462,928). Alternatively, H-boroPro may be produced by anew procedure (Kelly, T. A., et al., “The efficient synthesis and simpleresolution of a proline boronate ester suitable for enzyme inhibitionstudies,” Tetrahedron 49, 1009-1016 (1993)). Both of these syntheticroutes reportedly yield racemic H-boroPro pinanediol.

According to WO 98/00439, stereochemically pure L, L and L, Ddiastereomers of Z-Lys-boroPro are prepared by first resolving racemicH-boroPro through crystallization with optically active blockingprotecting groups ((1S,2S,3R,5S)-+-pinanediol isomer) followed bycoupling the isotopically pure L-boroPro and D-boroPro to thestereochemically pure L isomer of lysine (See U.S. Pat. No. 5,462,928).Alternatively, the L,L and L,D diastereomers of Lys-boroPro are preparedin high optical purity by coupling racemic H-boroPro by L-Lys andseparating the resulting diastereomeric Z-Lys-boroPro-diester into itscomponent L,D and L,L diastereomers using reverse phase HPLC aspreviously described for diastereomeric Pro-boroPro (W. G. Gutheil andW. W. Bachovchin, “Separation of L-Pro-DL-boroPro into Its ComponentDiastereomers and Kinetic Analysis of Their Inhibition of DipeptidylPeptidase IV. A New Method for the Analysis of Slow, Tight-BindingInhibition,” Biochemistry 32, 8723-8731 (1993)).

Example 5 Purification of Dipeptidyl Peptidase

The following examples are exemplary for dipeptidyl peptidase IV;dipeptidyl peptidase II may be isolated and used similarly according tothe methods of U.S. Pat. No. 6,485,955.

Porcine enzyme is purified as previously described (1), with severalmodifications. Kidneys from 15-20 animals are obtained, and the cortexdissected away and frozen at −80° C. Frozen tissue (2000-2500 g) ishomogenized in 12 L of 0.25 M sucrose in a Waring blender. Thehomogenate is left at 37° C. for 18 hours to facilitate cleavage of DPP4from cell membranes. After the cleavage step, the homogenate isclarified by centrifugation at 7000×g for 20 minutes at 4° C., and thesupernatant is collected. Solid ammonium sulfate is added to 60%saturation, and the precipitate is collected by centrifugation at10,000×g and discarded. Additional ammonium sulfate is added to thesupernatant to 80% saturation, and the 80% pellet is collected anddissolved in 20 mM Na₂HPO₄, pH 7.4.

After dialysis against 20 mM Na₂HPO₄, pH 7.4, the preparation isclarified by centrifugation at 10,000×g. The clarified preparation thenis applied to 300 ml of ConA Sepharose equilibrated in the same buffer.After washing with buffer to a constant A280, the column is eluted with5% (wt/vol) methyl α-D-mannopyranoside. Active fractions are pooled,concentrated, and dialyzed against 5 mM sodium acetate, pH 5.0. Dialyzedmaterial is flowed through a 100 ml Pharmacia Resource S columnequilibrated in the same buffer. The flowthrough material is collectedand contained most of the enzyme activity. Active material again isconcentrated and dialyzed into 20 mM Na₂HPO₄, pH 7.4. Lastly, theconcentrated enzyme is chromatographed on a Pharmacia S-200 gelfiltration column to removed low molecular weight contaminants. Purityof column fractions is analyzed by reducing SDS-PAGE, and the purestfractions pooled and concentrated. Purified enzyme is stored in 20%glycerol at −80° C.

Example 6 Assay of Dipeptidyl Peptidase

Enzyme is assayed under steady-state conditions as previously describedin Nagatsu et al., Anal. Biochem. 74: 466-76, 1976 with BNP assubstrate, with the following modifications. Reactions contain, in afinal volume of 100 μL 100 mM ACES, 52 mM TRIS, 52 mM ethanolamine, 500μM substrate, 0.2% DMSO, and 4.5 nM enzyme at 25° C., pH 7.4. Foranalysis of positive compounds, steady-state kinetic inhibitionconstants are determined as a function of both substrate and inhibitorconcentration. Complete inhibition experiments contain 11 substrate and7 inhibitor concentrations, with triplicate determinations. For tightbinding inhibitors with K_(i) s less than 20 nM, the enzymeconcentration is reduced to 0.5 nM and reaction times are increased to120 minutes. Pooled datasets from the three plates are fitted to theappropriate equation for either competitive, noncompetitive oruncompetitive inhibition.

Example 7 Chemical Deglycosylation of Naturietic Peptides

50 μg of protein is incubated at 4° C. for 2 hours in the dark, with 100μl of trifluoromethanesulfonic acid/anisole (2:1, v/v) reagent in glasstubing saturated with N₂. The reaction is stopped by the addition of 60%(v/v) pyridine at −20° C. The protein is extensively dialysed against 25mM sodium phosphate buffer pH 7.0.

Example 8 Enzymatic Deglycosylation of Naturietic Peptides

To 40 μL of sample is added 24, 25× protease inhibitor cocktail (Sigmacat. # P2714), 1 μL O-glycanase (Prozyme cat. # GK80090), 3 μL sialidaseA (Prozyme cat. # GK80040), and 8 μL 200 mM sodium phosphate buffer pH7.0. The mixture is vortexed gently and incubated at 20° C. for 4 hours.

Example 9 Analysis of Natriuretic Peptides by Mass Spectrometry

Preparation of Antibody Capture Surface

3 μL of antibody solution (0.25 mg/mL anti-BNP monoclonal antibody inborate buffered saline pH 8.0 (“BBS”)) is applied to appropriate spotsof a PS10 ProteinChip array (Ciphergen cat. #C553-0044), and the chip isplaced in a humid chamber with gentle agitation at 20° C. for 3 hours.The antibody solution is removed, and the array spots are washed twicewith 3 μL of 1.5 mg/mL BSA/0.1% Triton X-100/0.5 M Tris-HCl pH 8.0. Atthe second wash, the chip is placed in a humid chamber without agitationat 20° C. for 3 hours. Following this wash, the array is immersed in 5mM HEPES pH 7.5, and the excess buffer is removed.

Capture of BNP

Using a BIOMEC robotic pipetting station (Beckman Instruments), thearray is washed with 150 μL 1% Triton X-100 in BBS for 10 minutes; 150μL 10% PEG300/0.1% Triton X-100 in BBS for 10 minutes; and 3× with 150μL 0.2% Triton X-100 in BBS for 5 minutes each. 40 μL 0.2% Triton X-100in BBS and 40 μL deglycosylated sample (or control sample) is appliedand incubated overnight at 4° C. with gentle agitation.

Application of Energy Absorbing Matrix and MS Analysis

Following this incubation, the array is washed 3× with 150 μL 1Murea/0.1% CHAPS/0.3M KCl/50 mM Tris-HCl pH 7.5 for 1 minute each; and 3×with 300 μL 5 mM HEPES pH 7.5 for 3 seconds each. Excess buffer isremoved, and the array is allowed to air dry until no sheen is visible.For low molecular weight analysis (M/Z<6000), 1 μL of 20%α-cyano-4-hydroxycinnamic acid (CHCA, Ciphergen cat. #C300-0001) in 0.5%trifluoroacetic acid (Pierce cat #28904)/50% acetonitrile (Pierce cat.#20062) is applied to appropriate spots as an energy absorbing matrix(“EAM”). For high molecular weight analysis (M/Z≧6000), 1 μL of 50%sinapinic acid (SPA, Ciphergen Cat. No. C300-0002) in 0.5%trifluoroacetic acid/50% acetonitrile is applied to appropriate spots asan EAM. Spots are allowed to air dry, and a second 1 μL drop of theappropriate EAM is applied.

MS spectra are acquired using a Ciphergen ProteinChip reader model PBSIIC. For low molecular weight analysis, the following instrumentparameters are used: high mass is set to 70 kDa optimized from 2 kDa to15 kDa; starting laser intensity is set to 165; starting detectorsensitivity is set to 9; mass deflector is set to 1 kDa; acquisitionmethod is set to SELDI quantitation; SELDI acquisition parameters=26,delta=10, transients per=18, ending position=76; and warming positionswith 5 shots at intensity=175. For high molecular weight analysis, thefollowing instrument parameters are used: high mass is set to 70 kDaoptimized from 3 kDa to 30 kDa; starting laser intensity is set to 200;starting detector sensitivity is set to 9; mass deflector is set to 2kDa; acquisition method is set to SELDI quantitation; SELDI acquisitionparameters=24, delta=10, transients per=13, ending position=74; andwarming positions with 3 shots at intensity=210.

Example 10 Inhibition of BNP Degradation

Two human plasma samples were individually divided into two tubes, toone of which the reversible DPP inhibitor Diprotin A (Ile-Pro-Ile) wasadded to a concentration of 1 mM. Each sample was spiked with humanBNP₇₇₋₁₀₈, and the mixture held at 4° C. overnight. Each sample wassubjected to antibody capture SELDI mass spectrometry as describedabove. The results are depicted in FIG. 1. Panels A (no addition) and B(Diprotin A) represent one plasma sample, and panels C (no addition) andD (Diprotin A) the second plasma sample. Capture was performed with anantibody that recognizes human BNP.

Full length BNP₇₇₋₁₀₈ would be expected to appear at a molecular weightof about 3466 Da (large arrowhead), and BNP₇₉₋₁₁₃₈ (in which cleavageoccurs following the penultimate proline) at about 3282 Da (smallarrowhead). Comparing panels A to B and C to D, the cleavage ofBNP₇₇₋₁₀₈ to BNP₇₉₋₄₀₈ is inhibited by the DPP inhibitor. A secondcleavage product, presumed to be BNP₇₉₋₁₀₆ at a molecular weight ofabout 2988 Da, is also inhibited by the Diprotin A treatment, with acorresponding increase in a cleavage product presumed to be BNP₇₇₋₁₀₆ ata molecular weight of about 3173 Da. Thus, removal of the amino terminalser-pro dipeptide is sensitive to the presence of a DPP inhibitor, whilea second carboxyl terminal dipeptide cleavage is not.

While the invention has been described and exemplified in sufficientdetail for those skilled in this art to make and use it, variousalternatives, modifications, and improvements should be apparent withoutdeparting from the spirit and scope of the invention.

One skilled in the art readily appreciates that the present invention iswell adapted to carry out the objects and obtain the ends and advantagesmentioned, as well as those inherent therein. The examples providedherein are representative of preferred embodiments, are exemplary, andare not intended as limitations on the scope of the invention.Modifications therein and other uses will occur to those skilled in theart. These modifications are encompassed within the spirit of theinvention and are defined by the scope of the claims.

It will be readily apparent to a person skilled in the art that varyingsubstitutions and modifications may be made to the invention disclosedherein without departing from the scope and spirit of the invention.

All patents and publications mentioned in the specification areindicative of the levels of those of ordinary skill in the art to whichthe invention pertains. All patents and publications are hereinincorporated by reference to the same extent as if each individualpublication was specifically and individually indicated to beincorporated by reference.

The invention illustratively described herein suitably may be practicedin the absence of any element or elements, limitation or limitationswhich is not specifically disclosed herein. Thus, for example, in eachinstance herein any of the terms “comprising”, “consisting essentiallyof” and “consisting of” may be replaced with either of the other twoterms. The terms and expressions which have been employed are used asterms of description and not of limitation, and there is no intentionthat in the use of such terms and expressions of excluding anyequivalents of the features shown and described or portions thereof, butit is recognized that various modifications are possible within thescope of the invention claimed. Thus, it should be understood thatalthough the present invention has been specifically disclosed bypreferred embodiments and optional features, modification and variationof the concepts herein disclosed may be resorted to by those skilled inthe art, and that such modifications and variations are considered to bewithin the scope of this invention as defined by the appended claims.

Other embodiments are set forth within the following claims.

We claim:
 1. A method for the treatment of cardiovascular diseasecomprising administering to a subject in need of thereof, atherapeutically effective amount of a dipeptidyl peptidase inhibitor. 2.A method for the treatment of heart failure comprising administering toa subject in need thereof, a therapeutically effective amount of adipeptidyl peptidase inhibitor.
 3. Use of a dipeptidyl peptidaseinhibitor for the manufacture of a medicament for the treatment ofcardiovascular disease.
 4. Use of a dipeptidyl peptidase inhibitor forthe manufacture of a medicament for the treatment of heart failure. 5.Use according to claim 3 or 4, or method according to claim 1 or 2,wherein the dipeptidyl peptidase inhibitor inhibits DPP-IV.
 6. Useaccording to claim 3, or method according to claim 1, wherein thecardiovascular disease is stroke.
 7. Use according to claim 3, or methodaccording to claim 1, wherein the cardiovascular disease is acutemyocardial infarction.
 8. Use according to claim 3, or method accordingto claim 1, wherein the cardiovascular disease is systemic hypertension.9. Use according to claim 3, or method according to claim 1, wherein thecardiovascular disease is cardiac ischemia.
 10. A pharmaceuticalcomposition comprising a therapeutically effective amount of adipeptidyl peptidase inhibitor in combination with one or morepharmaceutically acceptable carriers for the treatment of cardiovasculardisease.
 11. A pharmaceutical composition comprising a therapeuticallyeffective amount of a dipeptidyl peptidase inhibitor in combination withone or more pharmaceutically acceptable carriers for the treatment ofheart failure.
 12. A pharmaceutical composition according to claim 10 or11, wherein the dipeptidyl peptidase inhibitor inhibits DPP-IV.
 13. Amethod of treating a subject in need of increased natriuretic peptidefunction, comprising: administering one or more analogues of B-typenatriuretic peptide that provide increased stability in the presence ofprolyl-specific DPP, relative to B-type natriuretic peptide.
 14. Amethod according to claim 13, wherein said subject suffers from one ormore conditions selected from the group consisting of stroke, congestiveheart failure, cardiac ischemia, systemic hypertension, and myocardialinfarction.
 15. A method according to claim 13, further comprisingadministering one or more inhibitors of prolyl-specific DPP to saidsubject.
 16. A method according to claim 13, further comprisingadministering one or more inhibitors of neutral endopeptidase to saidsubject.
 17. A method according to claim 15, further comprisingadministering one or more inhibitors of neutral endopeptidase to saidsubject.